Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-JGI_221_v2.0
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: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 149 of 168
Found at i:43960932 original size:22 final size:22
Alignment explanation
Indices: 43960904--43960945 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
43960894 GGCGCTTGTC
*
43960904 AAAGCGCCGCTAAAGGCCTAAA
1 AAAGCGCCGCTAAAAGCCTAAA
43960926 AAAGCGCCGCTAAAAGCCTA
1 AAAGCGCCGCTAAAAGCCTA
43960946 TTTTGGTGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.29, G:0.21, T:0.10
Consensus pattern (22 bp):
AAAGCGCCGCTAAAAGCCTAAA
Found at i:43965353 original size:22 final size:22
Alignment explanation
Indices: 43965325--43965375 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
43965315 ATTATATTAT
43965325 TCTCATGGCTAACGTACTAAGC
1 TCTCATGGCTAACGTACTAAGC
** *
43965347 TCTCATGTTTCACGTACTAAGC
1 TCTCATGGCTAACGTACTAAGC
43965369 TCTCATG
1 TCTCATG
43965376 TTTGAACAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.24, C:0.27, G:0.16, T:0.33
Consensus pattern (22 bp):
TCTCATGGCTAACGTACTAAGC
Found at i:43965376 original size:22 final size:22
Alignment explanation
Indices: 43965336--43965378 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
43965326 CTCATGGCTA
43965336 ACGTACTAAGCTCTCATGTTTC
1 ACGTACTAAGCTCTCATGTTTC
43965358 ACGTACTAAGCTCTCATGTTT
1 ACGTACTAAGCTCTCATGTTT
43965379 GAACAATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.23, C:0.26, G:0.14, T:0.37
Consensus pattern (22 bp):
ACGTACTAAGCTCTCATGTTTC
Found at i:43969325 original size:40 final size:40
Alignment explanation
Indices: 43969281--43969362 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
43969271 CAATATTGAC
43969281 ATAGAGCATCTGGTCTAAACCAGCATCTTTCTTCTGGATG
1 ATAGAGCATCTGGTCTAAACCAGCATCTTTCTTCTGGATG
43969321 ATAGAGCATCTGGTCTAAACCAGCATCTTTCTTCTGGATG
1 ATAGAGCATCTGGTCTAAACCAGCATCTTTCTTCTGGATG
43969361 AT
1 AT
43969363 CAGACCTCTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.33
Consensus pattern (40 bp):
ATAGAGCATCTGGTCTAAACCAGCATCTTTCTTCTGGATG
Found at i:43969717 original size:29 final size:29
Alignment explanation
Indices: 43969673--43969729 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
43969663 CTTCATCAAA
*
43969673 CTACTCACCAATGAGCCTTATGCTGTTGG
1 CTACTCACCAAGGAGCCTTATGCTGTTGG
*
43969702 CTACTCACCAAGGAGCCTTATGTTGTTG
1 CTACTCACCAAGGAGCCTTATGCTGTTG
43969730 ACCACAACCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.32
Consensus pattern (29 bp):
CTACTCACCAAGGAGCCTTATGCTGTTGG
Found at i:43974879 original size:21 final size:20
Alignment explanation
Indices: 43974855--43974897 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
43974845 AAATTTATTA
*
43974855 TTTATCATATTTTTAGTAATT
1 TTTATCATATGTTTAG-AATT
**
43974876 TTTATTTTATGTTTAGAATT
1 TTTATCATATGTTTAGAATT
43974896 TT
1 TT
43974898 AGTTATCTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.26, C:0.02, G:0.07, T:0.65
Consensus pattern (20 bp):
TTTATCATATGTTTAGAATT
Found at i:43976870 original size:28 final size:26
Alignment explanation
Indices: 43976838--43976894 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 26
43976828 GATAACAGGA
*
43976838 ATTAATTTCTGTTAGTTTATCTTTATAT
1 ATTAATTT-AGTTAGTTTA-CTTTATAT
* *
43976866 ATTAATTTAGTTATTTTAGTTTATAT
1 ATTAATTTAGTTAGTTTACTTTATAT
43976892 ATT
1 ATT
43976895 TTTTCAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 10 0.38
27 8 0.31
28 8 0.31
ACGTcount: A:0.28, C:0.04, G:0.07, T:0.61
Consensus pattern (26 bp):
ATTAATTTAGTTAGTTTACTTTATAT
Found at i:43979112 original size:13 final size:13
Alignment explanation
Indices: 43979094--43979118 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43979084 TTGAAAATAC
43979094 TTTTCAAAAGTGA
1 TTTTCAAAAGTGA
43979107 TTTTCAAAAGTG
1 TTTTCAAAAGTG
43979119 TGCTAGAAAA
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:0.36, C:0.08, G:0.16, T:0.40
Consensus pattern (13 bp):
TTTTCAAAAGTGA
Found at i:43980557 original size:29 final size:30
Alignment explanation
Indices: 43980498--43980555 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
43980488 TCCGAGCCTT
*
43980498 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
43980528 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
43980556 AGAGTCGAGG
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:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:43980786 original size:13 final size:13
Alignment explanation
Indices: 43980768--43980798 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
43980758 TTCCAGCAAC
43980768 TATGAATTTATTT
1 TATGAATTTATTT
43980781 TATGAATTTATTT
1 TATGAATTTATTT
*
43980794 GATGA
1 TATGA
43980799 TGATCTAAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (13 bp):
TATGAATTTATTT
Found at i:43980968 original size:50 final size:50
Alignment explanation
Indices: 43980893--43981085 Score: 296
Period size: 50 Copynumber: 3.8 Consensus size: 50
43980883 ATTTGGGTAA
43980893 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* *
43980943 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * *
43980993 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** *
43981043 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
43981086 TGTTATTATC
Statistics
Matches: 130, Mismatches: 12, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
50 96 0.74
51 34 0.26
ACGTcount: A:0.25, C:0.24, G:0.31, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:43983020 original size:23 final size:23
Alignment explanation
Indices: 43982964--43983021 Score: 77
Period size: 21 Copynumber: 2.6 Consensus size: 23
43982954 TAAGGAGGTG
43982964 TAATGCTCTCCTTTTAATGATATA
1 TAATGCTC-CCTTTTAATGATATA
43982988 -ACA-GCT-CCTTTTAATGATATA
1 TA-ATGCTCCCTTTTAATGATATA
43983009 TAATGCTCCCTTT
1 TAATGCTCCCTTT
43983022 GCATGTAACT
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
21 16 0.53
22 4 0.13
23 9 0.30
24 1 0.03
ACGTcount: A:0.28, C:0.21, G:0.09, T:0.43
Consensus pattern (23 bp):
TAATGCTCCCTTTTAATGATATA
Found at i:43983146 original size:9 final size:9
Alignment explanation
Indices: 43983129--43983194 Score: 73
Period size: 9 Copynumber: 7.2 Consensus size: 9
43983119 ACATTAAAAC
43983129 AAACACATT
1 AAACACATT
*
43983138 AATCACATTT
1 AAACACA-TT
*
43983148 AAACTCATT
1 AAACACATT
43983157 AAACACA--
1 AAACACATT
43983164 AAACACATT
1 AAACACATT
43983173 AAAAACACATT
1 --AAACACATT
43983184 AAACACATT
1 AAACACATT
43983193 AA
1 AA
43983195 GCTTAATAAG
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
7 7 0.15
9 25 0.52
10 7 0.15
11 9 0.19
ACGTcount: A:0.56, C:0.21, G:0.00, T:0.23
Consensus pattern (9 bp):
AAACACATT
Found at i:43983179 original size:11 final size:11
Alignment explanation
Indices: 43983163--43983194 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
43983153 CATTAAACAC
43983163 AAAACACATTA
1 AAAACACATTA
43983174 AAAACACATT-
1 AAAACACATTA
43983184 -AAACACATTA
1 AAAACACATTA
43983194 A
1 A
43983195 GCTTAATAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
9 9 0.47
11 10 0.53
ACGTcount: A:0.62, C:0.19, G:0.00, T:0.19
Consensus pattern (11 bp):
AAAACACATTA
Found at i:43988638 original size:24 final size:23
Alignment explanation
Indices: 43988605--43988674 Score: 63
Period size: 25 Copynumber: 3.0 Consensus size: 23
43988595 AAATAAAAAT
*
43988605 TTTTAATTTTCCTATTATTGTTATTA
1 TTTT-ATTTTCCTATT-TTATT-TTA
*
43988631 -TTTATTTTTACTATTTTATTTTA
1 TTTTA-TTTTCCTATTTTATTTTA
*
43988654 TTTTATTTTCAT-TTTTATTTT
1 TTTTATTTTCCTATTTTATTTT
43988675 TGCAGGAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
22 9 0.24
23 8 0.21
24 9 0.24
25 12 0.32
ACGTcount: A:0.20, C:0.06, G:0.01, T:0.73
Consensus pattern (23 bp):
TTTTATTTTCCTATTTTATTTTA
Found at i:43988639 original size:25 final size:24
Alignment explanation
Indices: 43988605--43988674 Score: 65
Period size: 24 Copynumber: 3.0 Consensus size: 24
43988595 AAATAAAAAT
* * *
43988605 TTTTAATTTTCCTATTATTGTTATTA
1 TTTTATTTTTACTATT-TTATT-TTA
43988631 -TTTATTTTTACTATTTTATTTTA
1 TTTTATTTTTACTATTTTATTTTA
*
43988654 TTTTATTTTCA-T-TTTTATTTT
1 TTTTATTTTTACTATTTTATTTT
43988675 TGCAGGAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
22 9 0.23
23 4 0.10
24 13 0.33
25 13 0.33
ACGTcount: A:0.20, C:0.06, G:0.01, T:0.73
Consensus pattern (24 bp):
TTTTATTTTTACTATTTTATTTTA
Found at i:43988640 original size:6 final size:6
Alignment explanation
Indices: 43988619--43988675 Score: 55
Period size: 6 Copynumber: 9.3 Consensus size: 6
43988609 AATTTTCCTA
* *
43988619 TTATTG TTATTAT TTATTT TTACTATT TTA-TT TTA-TT TTATTT TCATTT
1 TTATTT TTATT-T TTATTT TTA-T-TT TTATTT TTATTT TTATTT TTATTT
43988668 TTATTT TT
1 TTATTT TT
43988676 GCAGGAAAAC
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
5 10 0.23
6 23 0.52
7 6 0.14
8 5 0.11
ACGTcount: A:0.19, C:0.04, G:0.02, T:0.75
Consensus pattern (6 bp):
TTATTT
Found at i:43990321 original size:21 final size:21
Alignment explanation
Indices: 43990295--43990349 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
43990285 AACAGCGGTG
*
43990295 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGGTACTGTA
*
43990316 GCGGTGAGATTGGGTACTGTA
1 GCGGTGAGATTAGGTACTGTA
43990337 GCGGTGAGATTAG
1 GCGGTGAGATTAG
43990350 AAACAAAGTG
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:44002710 original size:8 final size:8
Alignment explanation
Indices: 44002697--44002723 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
44002687 TTTAAAATAC
44002697 TTTTTTAT
1 TTTTTTAT
44002705 TTTTTTAT
1 TTTTTTAT
44002713 TTTTTTAT
1 TTTTTTAT
44002721 TTT
1 TTT
44002724 AACCCGACCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (8 bp):
TTTTTTAT
Found at i:44009348 original size:22 final size:23
Alignment explanation
Indices: 44009320--44009363 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
44009310 GAACAATCTA
44009320 ATAAATATATAAATTT-ATTATC
1 ATAAATATATAAATTTAATTATC
*
44009342 ATAAATATATAAGTTTAATTAT
1 ATAAATATATAAATTTAATTAT
44009364 TATTTAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
ATAAATATATAAATTTAATTATC
Found at i:44009397 original size:33 final size:34
Alignment explanation
Indices: 44009360--44009427 Score: 102
Period size: 34 Copynumber: 2.0 Consensus size: 34
44009350 ATAAGTTTAA
*
44009360 TTATTATTTAATAT-AAAATAATTTAAATATATT
1 TTATTATTTAATATGAAAATAATTTAAAAATATT
* *
44009393 TTATTATTTATTATGAACATAATTTAAAAATATT
1 TTATTATTTAATATGAAAATAATTTAAAAATATT
44009427 T
1 T
44009428 AAATTTTATT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
33 13 0.42
34 18 0.58
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (34 bp):
TTATTATTTAATATGAAAATAATTTAAAAATATT
Found at i:44009531 original size:16 final size:16
Alignment explanation
Indices: 44009477--44009532 Score: 51
Period size: 16 Copynumber: 3.3 Consensus size: 16
44009467 TTTATAAAAA
44009477 TATAAATTTAACTTATG
1 TATAAATTTAA-TTATG
* *
44009494 TTATATTATTTAA-TATAA
1 -TATA-AATTTAATTAT-G
44009512 TATAAATTTAATTATG
1 TATAAATTTAATTATG
44009528 TATAA
1 TATAA
44009533 GATTATAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
16 11 0.35
17 10 0.32
18 4 0.13
19 6 0.19
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.50
Consensus pattern (16 bp):
TATAAATTTAATTATG
Found at i:44013345 original size:13 final size:13
Alignment explanation
Indices: 44013329--44013355 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
44013319 TTATATTTTT
44013329 GTTAAAATGGATG
1 GTTAAAATGGATG
44013342 GTTAAAATGGATG
1 GTTAAAATGGATG
44013355 G
1 G
44013356 AGAAGTTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.33, T:0.30
Consensus pattern (13 bp):
GTTAAAATGGATG
Found at i:44018098 original size:9 final size:9
Alignment explanation
Indices: 44018086--44018160 Score: 60
Period size: 9 Copynumber: 7.9 Consensus size: 9
44018076 ATAAAATTAT
44018086 TAAAAAATA
1 TAAAAAATA
44018095 TAAAAAATTA
1 TAAAAAA-TA
* *
44018105 TTAAAAGTA
1 TAAAAAATA
*
44018114 TAGAAAAGTTA
1 TA-AAAA-ATA
44018125 TAAAAAATA
1 TAAAAAATA
*
44018134 TTATAAAATA
1 -TAAAAAATA
*
44018144 TAAAACATA
1 TAAAAAATA
*
44018153 TAGAAAAT
1 TAAAAAAT
44018161 TGTTAAAAAT
Statistics
Matches: 52, Mismatches: 10, Indels: 8
0.74 0.14 0.11
Matches are distributed among these distances:
9 25 0.48
10 23 0.44
11 4 0.08
ACGTcount: A:0.65, C:0.01, G:0.05, T:0.28
Consensus pattern (9 bp):
TAAAAAATA
Found at i:44018129 original size:39 final size:37
Alignment explanation
Indices: 44018078--44018177 Score: 105
Period size: 39 Copynumber: 2.6 Consensus size: 37
44018068 ATAAGATGAT
*
44018078 AAAATTATTAAAAAATATAAAAAATTATTAAAA-GTATAG
1 AAAATTA-TAAAAAATATAAAAAA-TA-TAAAACATATAG
*
44018117 AAAAGTTATAAAAAATATTATAAAATATAAAACATATAG
1 AAAA-TTATAAAAAATA-TAAAAAATATAAAACATATAG
* *
44018156 AAAATTGTTAAAAAT-TAAAAAA
1 AAAATTATAAAAAATATAAAAAA
44018178 AAAGAGTTAC
Statistics
Matches: 53, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
36 6 0.11
38 14 0.26
39 24 0.45
40 9 0.17
ACGTcount: A:0.65, C:0.01, G:0.05, T:0.29
Consensus pattern (37 bp):
AAAATTATAAAAAATATAAAAAATATAAAACATATAG
Found at i:44018699 original size:19 final size:19
Alignment explanation
Indices: 44018675--44018767 Score: 70
Period size: 21 Copynumber: 4.8 Consensus size: 19
44018665 AATTTTTCTA
44018675 AATTTTTATATTTTATTTT
1 AATTTTTATATTTTATTTT
*
44018694 AGTTTTTATA---TATTTT
1 AATTTTTATATTTTATTTT
44018710 AATATTTTATATGCTTT-TTTT
1 AAT-TTTTATAT--TTTATTTT
*
44018731 AATTTTTAATATTTTTATTAT
1 AATTTTT-ATA-TTTTATTTT
*
44018752 ATTTATTTAT-TTTTAT
1 AATT-TTTATATTTTAT
44018768 CATTTTTTTC
Statistics
Matches: 60, Mismatches: 4, Indels: 20
0.71 0.05 0.24
Matches are distributed among these distances:
16 8 0.13
17 7 0.12
19 15 0.25
20 7 0.12
21 18 0.30
22 5 0.08
ACGTcount: A:0.27, C:0.01, G:0.02, T:0.70
Consensus pattern (19 bp):
AATTTTTATATTTTATTTT
Found at i:44018708 original size:29 final size:29
Alignment explanation
Indices: 44018667--44018773 Score: 80
Period size: 28 Copynumber: 3.8 Consensus size: 29
44018657 AAATTTATAA
* *
44018667 TTTTTCTAAATTTTTATATTTTATTTTAG
1 TTTTTATATATTTTTATATTTTATTTTAG
* *
44018696 TTTTTATATATTTTAATATTTTA-TAT-G
1 TTTTTATATATTTTTATATTTTATTTTAG
* *
44018723 CTTTTTTTA-ATTTTTAATATTTT-TATTA-
1 -TTTTTATATATTTTT-ATATTTTATTTTAG
* *
44018751 TATTTATTTATTTTTATCATTTT
1 TTTTTATATATTTTTAT-ATTTT
44018774 TTTCATGTGT
Statistics
Matches: 61, Mismatches: 11, Indels: 13
0.72 0.13 0.15
Matches are distributed among these distances:
27 13 0.21
28 28 0.46
29 20 0.33
ACGTcount: A:0.25, C:0.03, G:0.02, T:0.70
Consensus pattern (29 bp):
TTTTTATATATTTTTATATTTTATTTTAG
Found at i:44018719 original size:17 final size:16
Alignment explanation
Indices: 44018688--44018721 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
44018678 TTTTATATTT
*
44018688 TATTTTAGTTTTTATA
1 TATTTTAATTTTTATA
44018704 TATTTTAATATTTTATA
1 TATTTTAAT-TTTTATA
44018721 T
1 T
44018722 GCTTTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (16 bp):
TATTTTAATTTTTATA
Found at i:44018744 original size:9 final size:9
Alignment explanation
Indices: 44018676--44018774 Score: 60
Period size: 9 Copynumber: 10.7 Consensus size: 9
44018666 ATTTTTCTAA
44018676 ATTTTTA-T
1 ATTTTTATT
*
44018684 ATTTTATTTT
1 ATTTT-TATT
44018694 AGTTTTTA-T
1 A-TTTTTATT
*
44018703 ATATTTTAAT
1 AT-TTTTATT
*
44018713 ATTTTATATG
1 ATTTT-TATT
*
44018723 CTTTTT-TT
1 ATTTTTATT
*
44018731 AATTTTTAAT
1 -ATTTTTATT
44018741 ATTTTTATT
1 ATTTTTATT
*
44018750 ATATTTATTT
1 ATTTTTA-TT
*
44018760 ATTTTTATC
1 ATTTTTATT
44018769 ATTTTT
1 ATTTTT
44018775 TTCATGTGTC
Statistics
Matches: 70, Mismatches: 12, Indels: 17
0.71 0.12 0.17
Matches are distributed among these distances:
8 7 0.10
9 38 0.54
10 21 0.30
11 4 0.06
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (9 bp):
ATTTTTATT
Found at i:44023328 original size:19 final size:19
Alignment explanation
Indices: 44023304--44023376 Score: 128
Period size: 19 Copynumber: 3.8 Consensus size: 19
44023294 AATTTTTGAG
44023304 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
44023323 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
**
44023342 GATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
44023361 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
44023377 ATATATGACT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 50 1.00
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:44023988 original size:25 final size:25
Alignment explanation
Indices: 44023937--44023988 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
44023927 AATTTTTTTA
**
44023937 ATGTAATTATTATTATTATTTTCAT
1 ATGTAATTATTATTATTATTAGCAT
44023962 ATGTAATTATTATTATT-TTAGCTAT
1 ATGTAATTATTATTATTATTAGC-AT
44023987 AT
1 AT
44023989 ATATGTATAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 3 0.12
25 21 0.88
ACGTcount: A:0.33, C:0.04, G:0.06, T:0.58
Consensus pattern (25 bp):
ATGTAATTATTATTATTATTAGCAT
Found at i:44024112 original size:28 final size:28
Alignment explanation
Indices: 44024052--44024107 Score: 75
Period size: 25 Copynumber: 2.1 Consensus size: 28
44024042 TTTTTGCATA
44024052 TTTATTTTTTTAATATGAGATAATTATT
1 TTTATTTTTTTAATATGAGATAATTATT
44024080 TTTATTTTATTT-ATAT---ATAATTATT
1 TTTATTTT-TTTAATATGAGATAATTATT
44024105 TTT
1 TTT
44024108 TTTATAATCT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
25 12 0.44
28 12 0.44
29 3 0.11
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (28 bp):
TTTATTTTTTTAATATGAGATAATTATT
Found at i:44024676 original size:19 final size:20
Alignment explanation
Indices: 44024637--44024676 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
44024627 TTCTAGGCCT
* *
44024637 TTGTAATATTTATTATTGCA
1 TTGTAATATTTAATATAGCA
44024657 TTGT-ATATTTAATATAGCA
1 TTGTAATATTTAATATAGCA
44024676 T
1 T
44024677 CACTTCATTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.33, C:0.05, G:0.10, T:0.53
Consensus pattern (20 bp):
TTGTAATATTTAATATAGCA
Found at i:44025051 original size:98 final size:98
Alignment explanation
Indices: 44024917--44025111 Score: 300
Period size: 98 Copynumber: 2.0 Consensus size: 98
44024907 CTAAAAACAA
* * *
44024917 TAAAGGAAATATTCCGAATTTGAGATTTTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGAAAATATTCCGAATTTGAGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
44024982 TTAAATATTGGATAAATGGATGTTCTTTTAAAG
66 TTAAATATTGGATAAATGGATGTTCTTTTAAAG
* * * * *
44025015 TAAAGAAAATATTTCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATTTGGTGTGATTTC
1 TAAAGAAAATATTCCGAATTTGAGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
* *
44025080 TTAAATCTTGGATAAGTGGATGTTCTTTTAAA
66 TTAAATATTGGATAAATGGATGTTCTTTTAAA
44025112 ATTTTATTGT
Statistics
Matches: 87, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
98 87 1.00
ACGTcount: A:0.31, C:0.09, G:0.22, T:0.38
Consensus pattern (98 bp):
TAAAGAAAATATTCCGAATTTGAGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
TTAAATATTGGATAAATGGATGTTCTTTTAAAG
Found at i:44032409 original size:24 final size:24
Alignment explanation
Indices: 44032382--44032470 Score: 81
Period size: 25 Copynumber: 3.5 Consensus size: 24
44032372 AGCGAGCCAA
*
44032382 TATCGGGAAGCTCCGAAAGTCATT
1 TATCGGGAAGCTCCGAAAGCCATT
*
44032406 TATCGGGAAGCTCATGAAAGAGCC-TT
1 TATCGGGAAGCTC-CG-AA-AGCCATT
* *
44032432 TAATCGGGAAGCTTCGAAGAGCCATA
1 T-ATCGGGAAGCTCCGAA-AGCCATT
*
44032458 TATCAGGAAGCTC
1 TATCGGGAAGCTC
44032471 ATAAGAGCTA
Statistics
Matches: 53, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
24 13 0.25
25 18 0.34
26 8 0.15
27 14 0.26
ACGTcount: A:0.31, C:0.20, G:0.26, T:0.22
Consensus pattern (24 bp):
TATCGGGAAGCTCCGAAAGCCATT
Found at i:44032476 original size:25 final size:25
Alignment explanation
Indices: 44032328--44032478 Score: 84
Period size: 24 Copynumber: 6.1 Consensus size: 25
44032318 AGCTTTTTCA
* *
44032328 AGCCAT-TAACGGGAAGCTCATTAG
1 AGCCATATATCGGGAAGCTCATAAG
* * *
44032352 AGCTATA-ATCAGGAAG-TACA-AGCG
1 AGCCATATATCGGGAAGCT-CATA-AG
**
44032376 AGCCA-ATATCGGGAAGCTCCGAA-
1 AGCCATATATCGGGAAGCTCATAAG
* *
44032399 AGTCATTTATCGGGAAGCTCATGAAAG
1 AGCCATATATCGGGAAGCTCAT--AAG
* *
44032426 AGCC-TTTAATCGGGAAGCTTC-GAAG
1 AGCCATAT-ATCGGGAAGC-TCATAAG
*
44032451 AGCCATATATCAGGAAGCTCATAAG
1 AGCCATATATCGGGAAGCTCATAAG
44032476 AGC
1 AGC
44032479 TACGGTGTGT
Statistics
Matches: 95, Mismatches: 18, Indels: 27
0.68 0.13 0.19
Matches are distributed among these distances:
23 6 0.06
24 43 0.45
25 24 0.25
26 7 0.07
27 13 0.14
28 2 0.02
ACGTcount: A:0.35, C:0.20, G:0.25, T:0.20
Consensus pattern (25 bp):
AGCCATATATCGGGAAGCTCATAAG
Found at i:44032768 original size:27 final size:27
Alignment explanation
Indices: 44032733--44032790 Score: 116
Period size: 27 Copynumber: 2.1 Consensus size: 27
44032723 TATCGGACAT
44032733 TGTCGGATATGTGACTAATTTTCAACA
1 TGTCGGATATGTGACTAATTTTCAACA
44032760 TGTCGGATATGTGACTAATTTTCAACA
1 TGTCGGATATGTGACTAATTTTCAACA
44032787 TGTC
1 TGTC
44032791 AATTACACAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.38
Consensus pattern (27 bp):
TGTCGGATATGTGACTAATTTTCAACA
Found at i:44037544 original size:23 final size:22
Alignment explanation
Indices: 44037514--44037561 Score: 53
Period size: 23 Copynumber: 2.1 Consensus size: 22
44037504 ATTGTTCAAT
*
44037514 TAAGTTTACGA-ATACAAAATAA
1 TAAGTTTAAGAGA-ACAAAATAA
*
44037536 TAAGATTTAAGAGAATAAAATAA
1 TAAG-TTTAAGAGAACAAAATAA
44037559 TAA
1 TAA
44037562 ATGGGATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 4 0.18
23 17 0.77
24 1 0.05
ACGTcount: A:0.58, C:0.04, G:0.10, T:0.27
Consensus pattern (22 bp):
TAAGTTTAAGAGAACAAAATAA
Found at i:44044666 original size:26 final size:26
Alignment explanation
Indices: 44044631--44044764 Score: 93
Period size: 26 Copynumber: 5.3 Consensus size: 26
44044621 ACAGCTCTTA
*
44044631 TGAGCGTCCCGATATATGGCTCTTCG
1 TGAGCTTCCCGATATATGGCTCTTCG
* *
44044657 TGAGCTTCCCGAT-TAAAGGCTCTTTG
1 TGAGCTTCCCGATAT-ATGGCTCTTCG
* *
44044683 TGAGCTTCCTGAT-TAATGGCTCTCCG
1 TGAGCTTCCCGATAT-ATGGCTCTTCG
* * * *
44044709 -AAGCTTCTCG--ATATGGCTC-GCT
1 TGAGCTTCCCGATATATGGCTCTTCG
* * *
44044731 TGAACTTCCAGATATATGGCTATTCG
1 TGAGCTTCCCGATATATGGCTCTTCG
44044757 -GAGCTTCC
1 TGAGCTTCC
44044765 TGTTAATGGC
Statistics
Matches: 82, Mismatches: 20, Indels: 13
0.71 0.17 0.11
Matches are distributed among these distances:
22 1 0.01
23 13 0.16
24 1 0.01
25 23 0.28
26 44 0.54
ACGTcount: A:0.19, C:0.25, G:0.23, T:0.33
Consensus pattern (26 bp):
TGAGCTTCCCGATATATGGCTCTTCG
Found at i:44044793 original size:24 final size:24
Alignment explanation
Indices: 44044746--44044793 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
44044736 TTCCAGATAT
* * *
44044746 ATGGCTATTCGGAGCTTCCTGTTA
1 ATGGCTATTCGAAGCTACCCGTTA
*
44044770 ATGGCTTTTCGAAGCTACCCGTTA
1 ATGGCTATTCGAAGCTACCCGTTA
44044794 TTTGCTCGCA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.19, C:0.23, G:0.23, T:0.35
Consensus pattern (24 bp):
ATGGCTATTCGAAGCTACCCGTTA
Found at i:44046423 original size:24 final size:24
Alignment explanation
Indices: 44046391--44046438 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
44046381 TATTTGAAAT
44046391 ATCGATGGATACCCAGGTAGTACA
1 ATCGATGGATACCCAGGTAGTACA
44046415 ATCGATGGATACCCAGGTAGTACA
1 ATCGATGGATACCCAGGTAGTACA
44046439 CTCCAAGTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.21, G:0.25, T:0.21
Consensus pattern (24 bp):
ATCGATGGATACCCAGGTAGTACA
Found at i:44046678 original size:26 final size:26
Alignment explanation
Indices: 44046649--44046715 Score: 91
Period size: 26 Copynumber: 2.6 Consensus size: 26
44046639 ACATAGAAAT
44046649 TTTAATCAGGAAGCTCACGAAGAGCC
1 TTTAATCAGGAAGCTCACGAAGAGCC
* *
44046675 TTTAAACGGGAAGCTCACGAAGAGCC
1 TTTAATCAGGAAGCTCACGAAGAGCC
* *
44046701 ATTAGTCAGG-AGCTC
1 TTTAATCAGGAAGCTC
44046716 CGGATAGCCA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
25 5 0.14
26 30 0.86
ACGTcount: A:0.33, C:0.22, G:0.25, T:0.19
Consensus pattern (26 bp):
TTTAATCAGGAAGCTCACGAAGAGCC
Found at i:44046841 original size:65 final size:65
Alignment explanation
Indices: 44046765--44046905 Score: 192
Period size: 65 Copynumber: 2.2 Consensus size: 65
44046755 GGACTTGCAC
* * * *
44046765 AAAGAGCTGCGTTTGTGTCTGCAACATATGCAGGATCACAGCCGATCATAAAATAGGACGCTCAG
1 AAAGAGCTGCGTTTGTGTCCGCAACATATGCAAGATCACAACCGATCATAAAACAGGACGCTCAG
* * * * *
44046830 AAAGAGCTGCGTTTGTGTCCGCTATATATGCAAGATCACAACTGATCATATAACAGGACGCTCAT
1 AAAGAGCTGCGTTTGTGTCCGCAACATATGCAAGATCACAACCGATCATAAAACAGGACGCTCAG
*
44046895 AAAGAGTTGCG
1 AAAGAGCTGCG
44046906 GTAGCCCGCA
Statistics
Matches: 66, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
65 66 1.00
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.23
Consensus pattern (65 bp):
AAAGAGCTGCGTTTGTGTCCGCAACATATGCAAGATCACAACCGATCATAAAACAGGACGCTCAG
Found at i:44052870 original size:21 final size:21
Alignment explanation
Indices: 44052844--44052884 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
44052834 CACCATCATC
44052844 ATCAATATCAGCAGCAGCAGT
1 ATCAATATCAGCAGCAGCAGT
*
44052865 ATCAATATCATCAGCAGCAG
1 ATCAATATCAGCAGCAGCAG
44052885 CAACAACCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.39, C:0.24, G:0.17, T:0.20
Consensus pattern (21 bp):
ATCAATATCAGCAGCAGCAGT
Found at i:44059022 original size:71 final size:71
Alignment explanation
Indices: 44058906--44059050 Score: 254
Period size: 71 Copynumber: 2.0 Consensus size: 71
44058896 TAAGTATAAC
* * *
44058906 AACCTTGTAGTAATTGGATGCATAACAGAATGAGCTCCATTATGCACATTCTTTATGTACCAGAT
1 AACCTTGTACTAATTGGATGCATAACAGAATGAGCTCCACTATGCACATTCTTCATGTACCAGAT
44058971 GAGGAT
66 GAGGAT
*
44058977 AACCTTGTACTAATTGGATGCATAACAGAATGAGCTCCACTATGCACATTCTTCATGTATCAGAT
1 AACCTTGTACTAATTGGATGCATAACAGAATGAGCTCCACTATGCACATTCTTCATGTACCAGAT
44059042 GAGGAT
66 GAGGAT
44059048 AAC
1 AAC
44059051 TCCCTTCATG
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
71 70 1.00
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.30
Consensus pattern (71 bp):
AACCTTGTACTAATTGGATGCATAACAGAATGAGCTCCACTATGCACATTCTTCATGTACCAGAT
GAGGAT
Found at i:44060790 original size:5 final size:5
Alignment explanation
Indices: 44060763--44060829 Score: 70
Period size: 5 Copynumber: 14.2 Consensus size: 5
44060753 TTTTTATGTT
* *
44060763 TTATA -TATA TTAT- TT-TA TTATA TAATA TAATA -TATA TTATA TTATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
* *
44060809 TTATA TTGTT TTATA TTATA T
1 TTATA TTATA TTATA TTATA T
44060830 AAATTAAATA
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
3 1 0.02
4 11 0.21
5 40 0.77
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (5 bp):
TTATA
Found at i:44060800 original size:19 final size:19
Alignment explanation
Indices: 44060778--44060814 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
44060768 TATATTATTT
44060778 TATTATATAATATAATATA
1 TATTATATAATATAATATA
* *
44060797 TATTATATTATATTATAT
1 TATTATATAATATAATAT
44060815 TGTTTTATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TATTATATAATATAATATA
Found at i:44061895 original size:3 final size:3
Alignment explanation
Indices: 44061869--44061931 Score: 90
Period size: 3 Copynumber: 21.0 Consensus size: 3
44061859 GTGAGGTAAG
* * * *
44061869 TAT TAA TAT TAG TAT TAA TAT TAT TAT TAG TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
44061917 TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT
44061932 GAGTGGGAAT
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:44062102 original size:24 final size:26
Alignment explanation
Indices: 44062075--44062128 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 26
44062065 GTGAATTTGT
*
44062075 GAAATAATTATTG-ATTGAAAG-GTG-
1 GAAA-AATGATTGAATTGAAAGTGTGA
44062099 GAAAAATGATTGAATTGAAAGTGTGA
1 GAAAAATGATTGAATTGAAAGTGTGA
44062125 GAAA
1 GAAA
44062129 CNNNNNNNNN
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 7 0.27
24 12 0.46
25 3 0.12
26 4 0.15
ACGTcount: A:0.46, C:0.00, G:0.26, T:0.28
Consensus pattern (26 bp):
GAAAAATGATTGAATTGAAAGTGTGA
Found at i:44068397 original size:2 final size:2
Alignment explanation
Indices: 44068390--44068421 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
44068380 TACAAATGTG
44068390 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
44068422 AATAATGAAA
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:44073333 original size:4 final size:4
Alignment explanation
Indices: 44073324--44073348 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
44073314 ATTAGCTATT
44073324 AATA AATA AATA AATA AATA AATA A
1 AATA AATA AATA AATA AATA AATA A
44073349 CCTCCATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:44086952 original size:23 final size:23
Alignment explanation
Indices: 44086926--44086974 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
44086916 ATATAAATAA
*
44086926 TTAAAAACT-ATATATTTATTAAT
1 TTAAAAAATGATAT-TTTATTAAT
*
44086949 TTAAAAAATGATATTTTATTATT
1 TTAAAAAATGATATTTTATTAAT
44086972 TTA
1 TTA
44086975 TATATTTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
TTAAAAAATGATATTTTATTAAT
Found at i:44087001 original size:37 final size:38
Alignment explanation
Indices: 44086959--44087053 Score: 99
Period size: 37 Copynumber: 2.5 Consensus size: 38
44086949 TTAAAAAATG
*
44086959 ATATTTTATTATTTTATATATT-TAA-TATAAAGTTATA
1 ATATTTTATTATTTTATATATTAAAATTATAAA-TTATA
* *
44086996 CTATTTTATT-TTATTA-ATATTAAAATTATACATTATA
1 ATATTTTATTATT-TTATATATTAAAATTATAAATTATA
*
44087033 ATATTTTGTTATTTTAATATA
1 ATATTTTATTATTTT-ATATA
44087054 CATATTTTTA
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
36 7 0.15
37 29 0.62
38 8 0.17
39 3 0.06
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (38 bp):
ATATTTTATTATTTTATATATTAAAATTATAAATTATA
Found at i:44095790 original size:32 final size:33
Alignment explanation
Indices: 44095721--44095792 Score: 85
Period size: 35 Copynumber: 2.2 Consensus size: 33
44095711 CCGACGGCTA
* *
44095721 GCCCGAAATATGGGACGGTTTGGGTAAAAATATAG
1 GCCCGAAATATGGGAC-G-TTGGGTAAAAAAAGAG
44095756 GCCCGAAATATGGG-C-TTGGGTAAAAAAAGGAG
1 GCCCGAAATATGGGACGTTGGGTAAAAAAA-GAG
44095788 GCCCG
1 GCCCG
44095793 TTTAGAAAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
31 12 0.35
32 7 0.21
34 1 0.03
35 14 0.41
ACGTcount: A:0.33, C:0.15, G:0.33, T:0.18
Consensus pattern (33 bp):
GCCCGAAATATGGGACGTTGGGTAAAAAAAGAG
Found at i:44095919 original size:39 final size:40
Alignment explanation
Indices: 44095864--44096001 Score: 208
Period size: 39 Copynumber: 3.5 Consensus size: 40
44095854 AAATATATTT
* * *
44095864 ATTTTTTAAAATTTTAAAATATTTTTTACATACTTTTTGA
1 ATTTTTTAAAATTTTAAAATATTTTTAAAATACTTTTTTA
*
44095904 ATTTTTT-TAATTTTAAAATATTTTTAAAATACTTTTTTA
1 ATTTTTTAAAATTTTAAAATATTTTTAAAATACTTTTTTA
*
44095943 ATTTTTT-TAATTTTAAAATATTTTTAAAATACTTTTTTTA
1 ATTTTTTAAAATTTTAAAATATTTTTAAAATAC-TTTTTTA
44095983 ATTTTTTAAAATTTTAAAA
1 ATTTTTTAAAATTTTAAAA
44096002 ATAAAAATGG
Statistics
Matches: 91, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
39 60 0.66
40 21 0.23
41 10 0.11
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.59
Consensus pattern (40 bp):
ATTTTTTAAAATTTTAAAATATTTTTAAAATACTTTTTTA
Found at i:44095928 original size:11 final size:11
Alignment explanation
Indices: 44095914--44095994 Score: 59
Period size: 11 Copynumber: 7.8 Consensus size: 11
44095904 ATTTTTTTAA
44095914 TTTTAAAATAT
1 TTTTAAAATAT
44095925 TTTTAAAATACT
1 TTTTAAAATA-T
*
44095937 TTTT-TAAT-T
1 TTTTAAAATAT
*
44095946 TTTT----TAA
1 TTTTAAAATAT
44095953 TTTTAAAATAT
1 TTTTAAAATAT
44095964 TTTTAAAATACT
1 TTTTAAAATA-T
**
44095976 TTTTTTAAT-T
1 TTTTAAAATAT
44095986 TTTTAAAAT
1 TTTTAAAAT
44095995 TTTAAAAATA
Statistics
Matches: 56, Mismatches: 7, Indels: 15
0.72 0.09 0.19
Matches are distributed among these distances:
6 1 0.02
7 4 0.07
9 5 0.09
10 8 0.14
11 25 0.45
12 13 0.23
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:44095978 original size:28 final size:28
Alignment explanation
Indices: 44095925--44095978 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
44095915 TTTAAAATAT
* **
44095925 TTTTAAAATACTTTTTTAATTTTTTTAA
1 TTTTAAAATACTTTTTAAATACTTTTAA
44095953 TTTTAAAATA-TTTTTAAAATACTTTT
1 TTTTAAAATACTTTTT-AAATACTTTT
44095979 TTTAATTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 5 0.23
28 17 0.77
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (28 bp):
TTTTAAAATACTTTTTAAATACTTTTAA
Found at i:44095982 original size:31 final size:31
Alignment explanation
Indices: 44095944--44096004 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
44095934 ACTTTTTTAA
*
44095944 TTTTTTTAA-TTTTAAAATATTTTTAAAATAC
1 TTTTTTTAATTTTTAAAA-ATTTTAAAAATAC
*
44095975 TTTTTTTAATTTTTTAAAATTTTAAAAATA
1 TTTTTTTAATTTTTAAAAATTTTAAAAATA
44096005 AAAATGGGCC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 20 0.74
32 7 0.26
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (31 bp):
TTTTTTTAATTTTTAAAAATTTTAAAAATAC
Found at i:44099349 original size:20 final size:20
Alignment explanation
Indices: 44099326--44099411 Score: 73
Period size: 20 Copynumber: 4.3 Consensus size: 20
44099316 TACCAATAAG
*
44099326 TCTAACGGTTTACTAAAATT
1 TCTAACGGTTTACTAAAATA
* * *
44099346 TCTAAAGATTTATTAAAATA
1 TCTAACGGTTTACTAAAATA
* *
44099366 TCTAACGGTTTACCAATATA
1 TCTAACGGTTTACTAAAATA
* * * * *
44099386 ACTAAAGATTTACCAATATA
1 TCTAACGGTTTACTAAAATA
44099406 TCTAAC
1 TCTAAC
44099412 AATTTACAAA
Statistics
Matches: 52, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 52 1.00
ACGTcount: A:0.42, C:0.15, G:0.07, T:0.36
Consensus pattern (20 bp):
TCTAACGGTTTACTAAAATA
Found at i:44099370 original size:40 final size:39
Alignment explanation
Indices: 44099326--44099435 Score: 112
Period size: 40 Copynumber: 2.7 Consensus size: 39
44099316 TACCAATAAG
**
44099326 TCTAACGGTTTACTAAAATTTCTAAAGATTTATTAAAATA
1 TCTAACGGTTTAC-AAAATTTCTAAAGATTTACCAAAATA
* ** *
44099366 TCTAACGGTTTACCAATATAACTAAAGATTTACCAATATA
1 TCTAACGGTTTA-CAAAATTTCTAAAGATTTACCAAAATA
** *
44099406 TCTAACAATTTACAAATATTTCTAATGATT
1 TCTAACGGTTTACAAA-ATTTCTAAAGATT
44099436 GCTTTTTACC
Statistics
Matches: 56, Mismatches: 12, Indels: 4
0.78 0.17 0.06
Matches are distributed among these distances:
39 3 0.05
40 52 0.93
41 1 0.02
ACGTcount: A:0.42, C:0.14, G:0.06, T:0.38
Consensus pattern (39 bp):
TCTAACGGTTTACAAAATTTCTAAAGATTTACCAAAATA
Found at i:44099416 original size:20 final size:20
Alignment explanation
Indices: 44099363--44099430 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 20
44099353 ATTTATTAAA
**
44099363 ATATCTAACGGTTTACCAAT
1 ATATCTAACAATTTACCAAT
*
44099383 ATAACTAA-AGATTTACCAAT
1 ATATCTAACA-ATTTACCAAT
*
44099403 ATATCTAACAATTTACAAAT
1 ATATCTAACAATTTACCAAT
*
44099423 ATTTCTAA
1 ATATCTAA
44099431 TGATTGCTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
20 39 0.98
21 1 0.03
ACGTcount: A:0.44, C:0.16, G:0.04, T:0.35
Consensus pattern (20 bp):
ATATCTAACAATTTACCAAT
Found at i:44099553 original size:21 final size:20
Alignment explanation
Indices: 44099527--44099674 Score: 93
Period size: 20 Copynumber: 7.2 Consensus size: 20
44099517 GCCTTAACAA
44099527 TTACCAAAATTT-TGAAGGATT
1 TTACCAAAATTTAT-AAGGA-T
*
44099548 TTACCAATATTTATAAGGAT
1 TTACCAAAATTTATAAGGAT
* * * *
44099568 TTACTAAAATATCTAATGAT
1 TTACCAAAATTTATAAGGAT
* *
44099588 TTACCTAAAGATTTACCAAATGAT
1 TTACC-AAA-ATTTA--TAAGGAT
* * *
44099612 TAACCAAAATTTCTAAGAAT
1 TTACCAAAATTTATAAGGAT
* *
44099632 TTACTAAAATATT-TAACGAT
1 TTACCAAAAT-TTATAAGGAT
* *
44099652 TTACCAATATTTTTAAGGAT
1 TTACCAAAATTTATAAGGAT
44099672 TTA
1 TTA
44099675 TCAATATATC
Statistics
Matches: 98, Mismatches: 22, Indels: 15
0.73 0.16 0.11
Matches are distributed among these distances:
19 2 0.02
20 54 0.55
21 21 0.21
22 8 0.08
23 3 0.03
24 10 0.10
ACGTcount: A:0.42, C:0.11, G:0.08, T:0.39
Consensus pattern (20 bp):
TTACCAAAATTTATAAGGAT
Found at i:44099612 original size:12 final size:12
Alignment explanation
Indices: 44099582--44099619 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
44099572 TAAAATATCT
44099582 AATGATTTACCTA
1 AATGATTTACC-A
44099595 AA-GATTTACCA
1 AATGATTTACCA
*
44099606 AATGATTAACCA
1 AATGATTTACCA
44099618 AA
1 AA
44099620 ATTTCTAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
11 3 0.13
12 18 0.78
13 2 0.09
ACGTcount: A:0.47, C:0.16, G:0.08, T:0.29
Consensus pattern (12 bp):
AATGATTTACCA
Found at i:44099674 original size:40 final size:40
Alignment explanation
Indices: 44099609--44099774 Score: 140
Period size: 40 Copynumber: 4.1 Consensus size: 40
44099599 TTTACCAAAT
* * * *
44099609 GATTAACCAAAATTTCTAAGAATTTACT-AAAATATTTAAC
1 GATTTACCAATATTTCTAAGGATTTA-TAAAAATATCTAAC
* * *
44099649 GATTTACCAATATTTTTAAGGATTTATCAATATATCTAAC
1 GATTTACCAATATTTCTAAGGATTTATAAAAATATCTAAC
* * ** *
44099689 -ATTTTACTAATATTTTTAAGGATTTACCAATATATCTAAC
1 GA-TTTACCAATATTTCTAAGGATTTATAAAAATATCTAAC
* * *
44099729 GTTTTATCAGA-ATTTCTAAAGATTTATAAAAAATATCTAAC
1 GATTTACCA-ATATTTCTAAGGATTTAT-AAAAATATCTAAC
44099770 GATTT
1 GATTT
44099775 GTCAAAATTT
Statistics
Matches: 104, Mismatches: 17, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
39 2 0.02
40 86 0.83
41 16 0.15
ACGTcount: A:0.41, C:0.11, G:0.07, T:0.41
Consensus pattern (40 bp):
GATTTACCAATATTTCTAAGGATTTATAAAAATATCTAAC
Found at i:44099734 original size:20 final size:20
Alignment explanation
Indices: 44099630--44099734 Score: 95
Period size: 20 Copynumber: 5.2 Consensus size: 20
44099620 ATTTCTAAGA
* *
44099630 ATTTACTAAAATATTTAACG
1 ATTTACCAATATATTTAACG
* *
44099650 ATTTACCAATATTTTTAAGG
1 ATTTACCAATATATTTAACG
* *
44099670 ATTTATCAATATATCTAAC-
1 ATTTACCAATATATTTAACG
* * *
44099689 ATTTTACTAATATTTTTAAGG
1 A-TTTACCAATATATTTAACG
*
44099710 ATTTACCAATATATCTAACG
1 ATTTACCAATATATTTAACG
*
44099730 TTTTA
1 ATTTA
44099735 TCAGAATTTC
Statistics
Matches: 65, Mismatches: 18, Indels: 4
0.75 0.21 0.05
Matches are distributed among these distances:
19 1 0.02
20 63 0.97
21 1 0.02
ACGTcount: A:0.38, C:0.11, G:0.06, T:0.45
Consensus pattern (20 bp):
ATTTACCAATATATTTAACG
Found at i:44099747 original size:60 final size:59
Alignment explanation
Indices: 44099618--44099774 Score: 156
Period size: 60 Copynumber: 2.6 Consensus size: 59
44099608 TGATTAACCA
* * * *
44099618 AAATTTCTAAGAATTTACTAAAATATTTAACGATTTACCAATATTTTTAAGGATTTATC
1 AAATTTCTAACAATTTACTAAAATATTTAACGATTTACCAATATATCTAACGATTTATC
* * * * * *
44099677 AATATATCTAACATTTTACTAATATTTTTAAGGATTTACCAATATATCTAACGTTTTATC
1 AA-ATTTCTAACAATTTACTAAAATATTTAACGATTTACCAATATATCTAACGATTTATC
*
44099737 AGAATTTCTAA-AGATTTA-TAAAAAATATCTAACGATTT
1 A-AATTTCTAACA-ATTTACT--AAAATATTTAACGATTT
44099775 GTCAAAATTT
Statistics
Matches: 77, Mismatches: 16, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
59 4 0.05
60 59 0.77
61 14 0.18
ACGTcount: A:0.41, C:0.11, G:0.06, T:0.42
Consensus pattern (59 bp):
AAATTTCTAACAATTTACTAAAATATTTAACGATTTACCAATATATCTAACGATTTATC
Found at i:44099754 original size:20 final size:20
Alignment explanation
Indices: 44099616--44099787 Score: 66
Period size: 20 Copynumber: 8.6 Consensus size: 20
44099606 AATGATTAAC
44099616 CAAAATTTCT-AAGAATTTA-
1 CAAAATTTCTAAAG-ATTTAT
* *
44099635 CTAAAATATT-TAACGATTTAC
1 C-AAAAT-TTCTAAAGATTTAT
* * *
44099656 CAATATTTTTAAGGATTTAT
1 CAAAATTTCTAAAGATTTAT
* * *
44099676 CAATATATCT-AACATTT-T
1 CAAAATTTCTAAAGATTTAT
* * * *
44099694 ACTAATATTTTTAAGGATTTAC
1 -C-AAAATTTCTAAAGATTTAT
* * * *
44099716 CAATATATCTAACGTTTTAT
1 CAAAATTTCTAAAGATTTAT
*
44099736 CAGAATTTCTAAAGATTTAT
1 CAAAATTTCTAAAGATTTAT
* * * *
44099756 AAAAAATATCTAACGATTTGT
1 -CAAAATTTCTAAAGATTTAT
44099777 CAAAATTTCTA
1 CAAAATTTCTA
44099788 TTGTTTTTCC
Statistics
Matches: 113, Mismatches: 30, Indels: 19
0.70 0.19 0.12
Matches are distributed among these distances:
18 1 0.01
19 9 0.08
20 77 0.68
21 26 0.23
ACGTcount: A:0.41, C:0.12, G:0.06, T:0.41
Consensus pattern (20 bp):
CAAAATTTCTAAAGATTTAT
Found at i:44099781 original size:21 final size:21
Alignment explanation
Indices: 44099720--44099781 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
44099710 ATTTACCAAT
* *
44099720 ATATCTAACGTTTTATC-AGA
1 ATATCTAACGATTTATCAAAA
* * *
44099740 ATTTCTAAAGATTTATAAAAA
1 ATATCTAACGATTTATCAAAA
*
44099761 ATATCTAACGATTTGTCAAAA
1 ATATCTAACGATTTATCAAAA
44099782 TTTCTATTGT
Statistics
Matches: 32, Mismatches: 9, Indels: 1
0.76 0.21 0.02
Matches are distributed among these distances:
20 13 0.41
21 19 0.59
ACGTcount: A:0.44, C:0.11, G:0.08, T:0.37
Consensus pattern (21 bp):
ATATCTAACGATTTATCAAAA
Found at i:44099819 original size:20 final size:20
Alignment explanation
Indices: 44099796--44099844 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 20
44099786 TATTGTTTTT
*
44099796 CCAATATTTATGAGAATTTA
1 CCAATATTTATAAGAATTTA
* * *
44099816 CCAAAATTTCTAAGATTTTA
1 CCAATATTTATAAGAATTTA
*
44099836 CTAATATTT
1 CCAATATTT
44099845 TCAAAATTTC
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.39, C:0.12, G:0.06, T:0.43
Consensus pattern (20 bp):
CCAATATTTATAAGAATTTA
Found at i:44099934 original size:20 final size:20
Alignment explanation
Indices: 44099887--44100025 Score: 70
Period size: 20 Copynumber: 7.0 Consensus size: 20
44099877 AATTACAAAA
* * *
44099887 ATTTCTAAGGGTTTACAAAT
1 ATTTCTAAAGATTTACCAAT
* * *
44099907 AATACTAACGATTTACCAAT
1 ATTTCTAAAGATTTACCAAT
* *
44099927 ATTTCT--A-ATTTCACAAAC
1 ATTTCTAAAGATTT-ACCAAT
** * * *
44099945 AAATCTAACGATTTACTAAA
1 ATTTCTAAAGATTTACCAAT
*
44099965 ATTTCTAAAAATTTACCAAT
1 ATTTCTAAAGATTTACCAAT
* * * *
44099985 ATTTATAAGGGTTTACCAAA
1 ATTTCTAAAGATTTACCAAT
44100005 ATATTC-AAAGATTTACCAAT
1 AT-TTCTAAAGATTTACCAAT
44100025 A
1 A
44100026 AATCTTGATT
Statistics
Matches: 84, Mismatches: 30, Indels: 10
0.68 0.24 0.08
Matches are distributed among these distances:
17 4 0.05
18 8 0.10
20 66 0.79
21 6 0.07
ACGTcount: A:0.43, C:0.15, G:0.06, T:0.35
Consensus pattern (20 bp):
ATTTCTAAAGATTTACCAAT
Found at i:44100274 original size:20 final size:20
Alignment explanation
Indices: 44100251--44100380 Score: 102
Period size: 20 Copynumber: 6.4 Consensus size: 20
44100241 ATGTACTAGT
44100251 ATATCTAAGGATTTACCAAA
1 ATATCTAAGGATTTACCAAA
* *
44100271 ATATTTAATGATTTACCAAA
1 ATATCTAAGGATTTACCAAA
* * * *
44100291 ACTTTTTACA--ACTTACCAAT
1 A-TATCTA-AGGATTTACCAAA
* *
44100311 ATATGTAACGATTTACCAAA
1 ATATCTAAGGATTTACCAAA
* * *
44100331 AGATATAAGGGTTTACCAAA
1 ATATCTAAGGATTTACCAAA
*
44100351 ATATTTCTAAGGATTTACTAAA
1 ATA--TCTAAGGATTTACCAAA
44100373 ATATCTAA
1 ATATCTAA
44100381 ATTTCAATCA
Statistics
Matches: 87, Mismatches: 17, Indels: 12
0.75 0.15 0.10
Matches are distributed among these distances:
18 1 0.01
19 4 0.05
20 59 0.68
21 5 0.06
22 18 0.21
ACGTcount: A:0.43, C:0.14, G:0.08, T:0.35
Consensus pattern (20 bp):
ATATCTAAGGATTTACCAAA
Found at i:44107199 original size:30 final size:28
Alignment explanation
Indices: 44107163--44107262 Score: 112
Period size: 30 Copynumber: 3.4 Consensus size: 28
44107153 NNNNNNTTTT
*
44107163 TATTTTAAAAATTTTAAAAAATTAAAAAAG
1 TATTTT-AAAA-TTAAAAAAATTAAAAAAG
*
44107193 TATTTTAAAATTAAAAAAGTATTTTAAAAA-
1 TATTTTAAAATTAAAAAA--A-TTAAAAAAG
44107223 TATTTTAAAATTAAAAAAATTAAAAAAAG
1 TATTTTAAAATTAAAAAAATT-AAAAAAG
*
44107252 TATTTAAAAAT
1 TATTTTAAAAT
44107263 ATTTTAAAAT
Statistics
Matches: 61, Mismatches: 4, Indels: 11
0.80 0.05 0.14
Matches are distributed among these distances:
27 2 0.03
28 13 0.21
29 14 0.23
30 25 0.41
31 7 0.11
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (28 bp):
TATTTTAAAATTAAAAAAATTAAAAAAG
Found at i:44107222 original size:20 final size:20
Alignment explanation
Indices: 44107173--44107223 Score: 86
Period size: 19 Copynumber: 2.5 Consensus size: 20
44107163 TATTTTAAAA
44107173 ATTTTAAAAAATTAAAAAAGT
1 ATTTT-AAAAATTAAAAAAGT
44107194 ATTTT-AAAATTAAAAAAGT
1 ATTTTAAAAATTAAAAAAGT
44107213 ATTTTAAAAAT
1 ATTTTAAAAAT
44107224 ATTTTAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
19 19 0.66
20 5 0.17
21 5 0.17
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (20 bp):
ATTTTAAAAATTAAAAAAGT
Found at i:44107320 original size:39 final size:38
Alignment explanation
Indices: 44107199--44107322 Score: 196
Period size: 39 Copynumber: 3.2 Consensus size: 38
44107189 AAAGTATTTT
*
44107199 AAAATTAAAAAAGTATTTTAAAAATATTTTAAAATTAAA
1 AAAATAAAAAAAGTA-TTTAAAAATATTTTAAAATTAAA
44107238 AAAATTAAAAAAAGTATTTAAAAATATTTTAAAA-TAAA
1 AAAA-TAAAAAAAGTATTTAAAAATATTTTAAAATTAAA
*
44107276 AAAATAAAAAAAGTATGTAAAAAATATTTTAAAATTAAA
1 AAAATAAAAAAAGTAT-TTAAAAATATTTTAAAATTAAA
44107315 AAAATAAA
1 AAAATAAA
44107323 TATATTTATT
Statistics
Matches: 80, Mismatches: 2, Indels: 6
0.91 0.02 0.07
Matches are distributed among these distances:
37 12 0.15
38 24 0.30
39 34 0.43
40 10 0.12
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (38 bp):
AAAATAAAAAAAGTATTTAAAAATATTTTAAAATTAAA
Found at i:44111884 original size:21 final size:23
Alignment explanation
Indices: 44111841--44111893 Score: 65
Period size: 21 Copynumber: 2.3 Consensus size: 23
44111831 TATAAATTTG
44111841 AATTATTAAATTAACTTTAAAAAT
1 AATTA-TAAATTAACTTTAAAAAT
*
44111865 AATTATAATTTAA-TTT-AAAAT
1 AATTATAAATTAACTTTAAAAAT
*
44111886 TATTATAA
1 AATTATAA
44111894 CGTTACCATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 12 0.44
22 3 0.11
23 7 0.26
24 5 0.19
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (23 bp):
AATTATAAATTAACTTTAAAAAT
Found at i:44131336 original size:12 final size:12
Alignment explanation
Indices: 44131319--44131349 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
44131309 GAATGTACAG
44131319 AACATAAATAAT
1 AACATAAATAAT
44131331 AACATAAATAAT
1 AACATAAATAAT
*
44131343 AAAATAA
1 AACATAA
44131350 TAAGACATAG
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:0.71, C:0.06, G:0.00, T:0.23
Consensus pattern (12 bp):
AACATAAATAAT
Found at i:44131675 original size:14 final size:14
Alignment explanation
Indices: 44131592--44131676 Score: 61
Period size: 13 Copynumber: 6.3 Consensus size: 14
44131582 CCCTCCCTCT
*
44131592 TCTTCTTCTCCTTC
1 TCTTCTTCTTCTTC
* *
44131606 TCTTTTTCTTTTTC
1 TCTTCTTCTTCTTC
*
44131620 -CTTTTTCTTCTT-
1 TCTTCTTCTTCTTC
* * *
44131632 TCTGCTCCTCCTTCC
1 TCTTCTTCTTCTT-C
*
44131647 CCTTCTTCTTCTTC
1 TCTTCTTCTTCTTC
44131661 TCTTCTT-TTCTT-
1 TCTTCTTCTTCTTC
44131673 TCTT
1 TCTT
44131677 GCAGCTTCAT
Statistics
Matches: 55, Mismatches: 13, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
12 4 0.07
13 24 0.44
14 18 0.33
15 9 0.16
ACGTcount: A:0.00, C:0.35, G:0.01, T:0.64
Consensus pattern (14 bp):
TCTTCTTCTTCTTC
Found at i:44132772 original size:21 final size:22
Alignment explanation
Indices: 44132742--44132782 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
44132732 ATATCTAAAT
44132742 TACCACACACACATA-TATATA
1 TACCACACACACATACTATATA
*
44132763 TACCATACACACATACTATA
1 TACCACACACACATACTATA
44132783 AAACTTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.46, C:0.29, G:0.00, T:0.24
Consensus pattern (22 bp):
TACCACACACACATACTATATA
Found at i:44134809 original size:28 final size:31
Alignment explanation
Indices: 44134777--44134835 Score: 79
Period size: 28 Copynumber: 2.0 Consensus size: 31
44134767 TGTTTTGTTT
44134777 TTATTATAATAA-CATTAT-AAT-ATATAAA
1 TTATTATAATAACCATTATAAATAATATAAA
* *
44134805 TTATTATTATAACCTTTATAAATAATATAAA
1 TTATTATAATAACCATTATAAATAATATAAA
44134836 AACTATATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 11 0.42
29 5 0.19
30 3 0.12
31 7 0.27
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (31 bp):
TTATTATAATAACCATTATAAATAATATAAA
Found at i:44136981 original size:98 final size:100
Alignment explanation
Indices: 44136835--44137033 Score: 332
Period size: 98 Copynumber: 2.0 Consensus size: 100
44136825 CGAGCCAGTT
*
44136835 CCATTTTCACTCTCTCCAAAGTAAATTTTCTTTTCCTCTTTTCTGTTCAAGTTCAAGATTGTTCA
1 CCATTTTCACTCTCTCCAAAGTAAATTTTCTTTTCCTCTTTTCTGTTCAACTTCAAGATTGTTCA
*
44136900 GTGATTAATTTGCACGCCAAGTAAAT-TTTTTTTC
66 GCGATTAATTTGCACGCCAAGTAAATCTTTTTTTC
44136934 CCATTTTCACTCTCTCCAAAGT-AATTTAT-TTTTCCTCTTTTCTGTTCAACTTCAAGATTGTTC
1 CCATTTTCACTCTCTCCAAAGTAAATTT-TCTTTTCCTCTTTTCTGTTCAACTTCAAGATTGTTC
* *
44136997 AGCGATTAATTTTCACGCCAAGTAATTCTTTTTTTC
65 AGCGATTAATTTGCACGCCAAGTAAATCTTTTTTTC
44137033 C
1 C
44137034 GTAATGGGTG
Statistics
Matches: 94, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
98 62 0.66
99 32 0.34
ACGTcount: A:0.23, C:0.23, G:0.09, T:0.46
Consensus pattern (100 bp):
CCATTTTCACTCTCTCCAAAGTAAATTTTCTTTTCCTCTTTTCTGTTCAACTTCAAGATTGTTCA
GCGATTAATTTGCACGCCAAGTAAATCTTTTTTTC
Found at i:44140846 original size:15 final size:15
Alignment explanation
Indices: 44140817--44140855 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
44140807 AAATATAATT
44140817 ATTTTTAGTAAATATA
1 ATTTTTA-TAAATATA
*
44140833 ATTTTTATATATATA
1 ATTTTTATAAATATA
*
44140848 ATATTTAT
1 ATTTTTAT
44140856 TTTTCAATCC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (15 bp):
ATTTTTATAAATATA
Found at i:44140853 original size:17 final size:18
Alignment explanation
Indices: 44140807--44140853 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 18
44140797 AATTATTACC
44140807 AAATATAATTATTTTTAGT
1 AAATATAA-TATTTTTAGT
44140826 AAATAT-A-ATTTTTA-T
1 AAATATAATATTTTTAGT
*
44140841 ATATATAATATTT
1 AAATATAATATTT
44140854 ATTTTTCAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
15 6 0.24
16 8 0.32
17 4 0.16
18 1 0.04
19 6 0.24
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (18 bp):
AAATATAATATTTTTAGT
Found at i:44141328 original size:51 final size:50
Alignment explanation
Indices: 44141245--44141345 Score: 152
Period size: 51 Copynumber: 2.0 Consensus size: 50
44141235 TAAATAAAAG
44141245 ATTTATTAATTAAAAAGATAAATAAAAATAAAAAAA-CTTGAAAACAATAT
1 ATTTATTAATTAAAAAGATAAATAAAAATAAAAAAAGCTTG-AAACAATAT
*
44141295 ATTTATTAATTAAAAA-ATTTAATTAAAAATAAAAAAAGCTTGAAACAATAT
1 ATTTATTAATTAAAAAGA--TAAATAAAAATAAAAAAAGCTTGAAACAATAT
44141346 TAAATAAAAG
Statistics
Matches: 47, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
49 1 0.02
50 16 0.34
51 26 0.55
52 4 0.09
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.31
Consensus pattern (50 bp):
ATTTATTAATTAAAAAGATAAATAAAAATAAAAAAAGCTTGAAACAATAT
Found at i:44141526 original size:50 final size:52
Alignment explanation
Indices: 44141466--44141579 Score: 133
Period size: 51 Copynumber: 2.2 Consensus size: 52
44141456 ATTGATATAA
* * *
44141466 TAACAAATTTAG-CCTCAACGTTTACACATTCTATCAATTTGGTATTT-ATT
1 TAACAAATTTAGCCCGCAACATTTACACATTCTATCAATTTGATATTTGATT
* * * * *
44141516 TAACAAATTTAGCCCGCAATATTTATACATTTTGTCAATTTGATCTTTGATT
1 TAACAAATTTAGCCCGCAACATTTACACATTCTATCAATTTGATATTTGATT
*
44141568 TAATAAATTTAG
1 TAACAAATTTAG
44141580 TCCACAATAT
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
50 12 0.23
51 27 0.51
52 14 0.26
ACGTcount: A:0.33, C:0.15, G:0.09, T:0.43
Consensus pattern (52 bp):
TAACAAATTTAGCCCGCAACATTTACACATTCTATCAATTTGATATTTGATT
Found at i:44141579 original size:52 final size:51
Alignment explanation
Indices: 44141499--44141598 Score: 128
Period size: 52 Copynumber: 1.9 Consensus size: 51
44141489 ACACATTCTA
* * **
44141499 TCAATTTGGTATTTATTTAACAAATTTAGCCCGCAATATTTATACATTTTG
1 TCAATTTGATATTTATTTAACAAATTTAGCCCACAATATCAATACATTTTG
* * *
44141550 TCAATTTGATCTTTGATTTAATAAATTTAGTCCACAATATCAATACATT
1 TCAATTTGATATTT-ATTTAACAAATTTAGCCCACAATATCAATACATT
44141599 CCGTTAATAT
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
51 12 0.29
52 29 0.71
ACGTcount: A:0.34, C:0.14, G:0.08, T:0.44
Consensus pattern (51 bp):
TCAATTTGATATTTATTTAACAAATTTAGCCCACAATATCAATACATTTTG
Found at i:44153320 original size:29 final size:29
Alignment explanation
Indices: 44153287--44153344 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
44153277 TTTCAATCGA
*
44153287 GTAGTTTTCTCCGCTATCCTCAAGCTCAC
1 GTAGTCTTCTCCGCTATCCTCAAGCTCAC
*
44153316 GTAGTCTTCTCCGCTATCCTGAAGCTCAC
1 GTAGTCTTCTCCGCTATCCTCAAGCTCAC
44153345 ATCTGTTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.17, C:0.34, G:0.16, T:0.33
Consensus pattern (29 bp):
GTAGTCTTCTCCGCTATCCTCAAGCTCAC
Found at i:44157463 original size:18 final size:18
Alignment explanation
Indices: 44157381--44157463 Score: 62
Period size: 18 Copynumber: 4.3 Consensus size: 18
44157371 TAATGTTATC
44157381 ATTATTTTTACTACTATT
1 ATTATTTTTACTACTATT
*
44157399 ATTATGTTTAATACTATTATCACT
1 ATTAT-TTT--TACTACTAT---T
* *
44157423 ATTATTTTT-TTA-TTTT
1 ATTATTTTTACTACTATT
44157439 ATATATTTTTACTACTATT
1 AT-TATTTTTACTACTATT
44157458 ATTATT
1 ATTATT
44157464 ATTCTTATTT
Statistics
Matches: 51, Mismatches: 5, Indels: 18
0.69 0.07 0.24
Matches are distributed among these distances:
16 3 0.06
17 7 0.14
18 11 0.22
19 10 0.20
20 2 0.04
21 9 0.18
23 3 0.06
24 6 0.12
ACGTcount: A:0.29, C:0.08, G:0.01, T:0.61
Consensus pattern (18 bp):
ATTATTTTTACTACTATT
Found at i:44158266 original size:46 final size:41
Alignment explanation
Indices: 44158187--44158626 Score: 316
Period size: 46 Copynumber: 10.7 Consensus size: 41
44158177 TACGTATGAT
*
44158187 CACTTATCACTTGTTC-C-TGATCAGATAAGTGTAGCTAAGGCTAC
1 CACTTATCACTTTTTCACTTGATCAGATAA--GTAG-TAA-G-TAC
* *
44158231 CACTTATCACTTTGTCACTTGATAAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTTTCACTTGATCAGATAA--GTAG-T-AAG-TAC
*
44158277 CACTTATCACTTTGTCACTTGATCAGATAAGTA-T-AG---
1 CACTTATCACTTTTTCACTTGATCAGATAAGTAGTAAGTAC
44158313 CACTTATCACTTTTTCACTTGATCAGATAAGT-GT-AG---
1 CACTTATCACTTTTTCACTTGATCAGATAAGTAGTAAGTAC
44158349 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTTTCACTTGATCAGATAA--GTAG-T-AAG-TAC
* * *
44158395 CACTTATCACTTTATCTCTTGATCAAATAAGT-GT-AG---
1 CACTTATCACTTTTTCACTTGATCAGATAAGTAGTAAGTAC
* *
44158431 CACTTATCACTTTTTCACTTGATTAGATAAG-A-TAAGTGTAG
1 CACTTATCACTTTTTCACTTGATCAGATAAGTAGTAA--GTAC
* *
44158472 CACTTATCATTTTTTCACTTGATTAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTTTCACTTGATCAGATAA--GTAG-T-AAG-TAC
* * *
44158518 CATTTATCACTTTGTCTCTTGATCAGATAAGT-GT-AG---
1 CACTTATCACTTTTTCACTTGATCAGATAAGTAGTAAGTAC
*
44158554 CACTTATCATTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTTTCACTTGATCAGATAA--GTAG-T-AAG-TAC
* *
44158600 CACTTATCACTTTATCTCTTGATCAGA
1 CACTTATCACTTTTTCACTTGATCAGA
44158627 AGTACTCAAA
Statistics
Matches: 332, Mismatches: 26, Indels: 74
0.77 0.06 0.17
Matches are distributed among these distances:
35 1 0.00
36 118 0.36
38 5 0.02
39 2 0.01
40 8 0.02
41 29 0.09
42 7 0.02
43 3 0.01
44 22 0.07
45 2 0.01
46 131 0.39
47 4 0.01
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.37
Consensus pattern (41 bp):
CACTTATCACTTTTTCACTTGATCAGATAAGTAGTAAGTAC
Found at i:44158318 original size:36 final size:36
Alignment explanation
Indices: 44158277--44158590 Score: 277
Period size: 36 Copynumber: 8.0 Consensus size: 36
44158267 CTAAAGCTAC
*
44158277 CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
1 CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
*
44158313 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAG
1 CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
44158349 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAG
1 CACTTATCACTTTTTCACTTGATCAGATAA--GTA--T--AG
* * * *
44158391 CTACCACTTATCACTTTATCTCTTGATCAAATAAGTGTAG
1 ----CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
*
44158431 CACTTATCACTTTTTCACTTGATTAGATAAGATAAGTGTAG
1 CACTTATCACTTTTTCACTTGATCAGATAAG-T-A---TAG
* *
44158472 CACTTATCATTTTTTCACTTGATTAGATAAGTGTAGCTAAAG
1 CACTTATCACTTTTTCACTTGATCAGATAA--GTA--T--AG
* * *
44158514 CTACCATTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
1 C-A-C--TTATCACTTTTTCACTTGATCAGATAAGTATAG
* *
44158554 CACTTATCATTTTTTCACTTGATCAGATAAGTGTAG
1 CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
44158590 C
1 C
44158591 TAAAGCTACC
Statistics
Matches: 232, Mismatches: 23, Indels: 46
0.77 0.08 0.15
Matches are distributed among these distances:
36 122 0.53
37 1 0.00
38 3 0.01
39 1 0.00
40 7 0.03
41 33 0.14
42 8 0.03
43 2 0.01
44 5 0.02
46 50 0.22
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (36 bp):
CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
Found at i:44158525 original size:123 final size:123
Alignment explanation
Indices: 44158231--44158584 Score: 565
Period size: 123 Copynumber: 2.9 Consensus size: 123
44158221 CTAAGGCTAC
* *
44158231 CACTTATCACTTTGTCACTTGATAAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACT
1 CACTTATCACTTTTTCACTTGATAAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
* *
44158296 TGATCAGATAAGTATAGCACTTATCACTTTTTCAC----TT-GATCAGATAAGTGTAG
66 TGATCAGATAAGTGTAGCACTTATCACTTTTTCACTTGATTAGATAAGATAAGTGTAG
* *
44158349 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATCTCT
1 CACTTATCACTTTTTCACTTGATAAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
*
44158414 TGATCAAATAAGTGTAGCACTTATCACTTTTTCACTTGATTAGATAAGATAAGTGTAG
66 TGATCAGATAAGTGTAGCACTTATCACTTTTTCACTTGATTAGATAAGATAAGTGTAG
* * *
44158472 CACTTATCATTTTTTCACTTGATTAGATAAGTGTAGCTAAAGCTACCATTTATCACTTTGTCTCT
1 CACTTATCACTTTTTCACTTGATAAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
* *
44158537 TGATCAGATAAGTGTAGCACTTATCATTTTTTCACTTGATCAGATAAG
66 TGATCAGATAAGTGTAGCACTTATCACTTTTTCACTTGATTAGATAAG
44158585 TGTAGCTAAA
Statistics
Matches: 217, Mismatches: 14, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
118 94 0.43
122 2 0.01
123 121 0.56
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.38
Consensus pattern (123 bp):
CACTTATCACTTTTTCACTTGATAAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
TGATCAGATAAGTGTAGCACTTATCACTTTTTCACTTGATTAGATAAGATAAGTGTAG
Found at i:44158591 original size:82 final size:82
Alignment explanation
Indices: 44158231--44158626 Score: 376
Period size: 82 Copynumber: 4.9 Consensus size: 82
44158221 CTAAGGCTAC
* * * * *
44158231 CACTTATCACTTTGTCACTTGATAAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACT
1 CACTTATCATTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATCTCT
*
44158296 TGATCAGATAAGTATAG
66 TGATCAGATAAGTGTAG
* * *
44158313 CACTTATCACTTTTTCACTTGATCAGATAA--GT-G-T--AG----CACTTATCACTTTTTCACT
1 CACTTATCATTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATCTCT
44158368 TGATCAGATAAGTGTAGCTAAAG
66 TGATCAGATAA--GT-G-T--AG
* * * * * * *
44158391 CTACCACTTATCACTTTATCTCTTGATCAAATAAGTGTAGC---A-CTTATCACTTTTTCACTTG
1 ----CACTTATCATTTTTTCACTTGATCAGATAAGTGTAGCTAAAGC-TACCAC-TTATCACTTT
* *
44158452 A--T-TAGATAAGATAAGTGTAG
60 ATCTCTTGATCAGATAAGTGTAG
* * *
44158472 CACTTATCATTTTTTCACTTGATTAGATAAGTGTAGCTAAAGCTACCATTTATCACTTTGTCTCT
1 CACTTATCATTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATCTCT
44158537 TGATCAGATAAGTGTAG
66 TGATCAGATAAGTGTAG
44158554 CACTTATCATTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATCTCT
1 CACTTATCATTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATCTCT
44158619 TGATCAGA
66 TGATCAGA
44158627 AGTACTCAAA
Statistics
Matches: 259, Mismatches: 28, Indels: 54
0.76 0.08 0.16
Matches are distributed among these distances:
72 29 0.11
74 2 0.01
76 3 0.01
77 32 0.12
78 3 0.01
79 9 0.03
80 7 0.03
81 4 0.02
82 141 0.54
83 1 0.00
84 3 0.01
85 4 0.02
87 10 0.04
89 3 0.01
90 8 0.03
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (82 bp):
CACTTATCATTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATCTCT
TGATCAGATAAGTGTAG
Found at i:44161284 original size:12 final size:12
Alignment explanation
Indices: 44161269--44161319 Score: 61
Period size: 12 Copynumber: 4.4 Consensus size: 12
44161259 TATGTGTATT
44161269 TATATATTTATA
1 TATATATTTATA
*
44161281 TATATATATATA
1 TATATATTTATA
44161293 TATAT-TTTA-A
1 TATATATTTATA
* *
44161303 TACATATTTACA
1 TATATATTTATA
44161315 TATAT
1 TATAT
44161320 CTAAATACCC
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
10 5 0.15
11 7 0.21
12 21 0.64
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (12 bp):
TATATATTTATA
Found at i:44162982 original size:23 final size:21
Alignment explanation
Indices: 44162948--44162989 Score: 66
Period size: 23 Copynumber: 1.9 Consensus size: 21
44162938 TAATTTAATC
44162948 AAAAATATAAATTTAAAAGCT
1 AAAAATATAAATTTAAAAGCT
44162969 AAAAATATAAAAATTTAAAAG
1 AAAAATAT--AAATTTAAAAG
44162990 AAAAACTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 8 0.42
23 11 0.58
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (21 bp):
AAAAATATAAATTTAAAAGCT
Found at i:44162993 original size:21 final size:20
Alignment explanation
Indices: 44162947--44162994 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 20
44162937 TTAATTTAAT
44162947 CAAAAATATAAATTTAAAAG
1 CAAAAATATAAATTTAAAAG
44162967 CTAAAAATATAAAAATTTAAAAG
1 C-AAAAATAT--AAATTTAAAAG
44162990 -AAAAA
1 CAAAAA
44162995 CTAAAATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
20 1 0.04
21 13 0.52
23 11 0.44
ACGTcount: A:0.69, C:0.04, G:0.04, T:0.23
Consensus pattern (20 bp):
CAAAAATATAAATTTAAAAG
Found at i:44171422 original size:15 final size:16
Alignment explanation
Indices: 44171402--44171434 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
44171392 TAACAAAAAA
44171402 AAAATCC-TTAACTTC
1 AAAATCCATTAACTTC
44171417 AAAATCCTATTAACTTC
1 AAAATCC-ATTAACTTC
44171434 A
1 A
44171435 TTTTCGTGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
17 9 0.56
ACGTcount: A:0.42, C:0.24, G:0.00, T:0.33
Consensus pattern (16 bp):
AAAATCCATTAACTTC
Found at i:44177096 original size:18 final size:16
Alignment explanation
Indices: 44177073--44177111 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 16
44177063 AATGAAAATA
44177073 AATAAATAAATCATTTTT
1 AATAAATAAA-C-TTTTT
*
44177091 AATAAATATACTTTTT
1 AATAAATAAACTTTTT
44177107 AATAA
1 AATAA
44177112 TTTTTTTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 10 0.50
17 1 0.05
18 9 0.45
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (16 bp):
AATAAATAAACTTTTT
Found at i:44177392 original size:13 final size:13
Alignment explanation
Indices: 44177376--44177426 Score: 52
Period size: 13 Copynumber: 3.8 Consensus size: 13
44177366 ATAATACATT
44177376 TAAATAATTATAA
1 TAAATAATTATAA
44177389 TAAA-AATTAATATTA
1 TAAATAATT-ATA--A
44177404 TAAATAGATTA-AA
1 TAAATA-ATTATAA
44177417 TAAATAATTA
1 TAAATAATTA
44177427 GAAAAAATGG
Statistics
Matches: 33, Mismatches: 0, Indels: 11
0.75 0.00 0.25
Matches are distributed among these distances:
12 8 0.24
13 14 0.42
15 6 0.18
16 2 0.06
17 3 0.09
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (13 bp):
TAAATAATTATAA
Found at i:44183031 original size:27 final size:27
Alignment explanation
Indices: 44182999--44183052 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
44182989 CCAGCTTAAA
*
44182999 AAAGTAAAGAACTTCTGATGTTCAGGT
1 AAAGTAAAGAACTTATGATGTTCAGGT
44183026 AAAGTAAAGAACTTATGATGTTCAGGT
1 AAAGTAAAGAACTTATGATGTTCAGGT
44183053 TCAATGTTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.39, C:0.09, G:0.22, T:0.30
Consensus pattern (27 bp):
AAAGTAAAGAACTTATGATGTTCAGGT
Found at i:44189243 original size:37 final size:37
Alignment explanation
Indices: 44189199--44189291 Score: 177
Period size: 37 Copynumber: 2.5 Consensus size: 37
44189189 CACTTGTCCC
44189199 TGATCAGATAAGTGTAGCCACCTATCACTTTGTTTCT
1 TGATCAGATAAGTGTAGCCACCTATCACTTTGTTTCT
*
44189236 TGATCAGATAAGTGTAGCCACTTATCACTTTGTTTCT
1 TGATCAGATAAGTGTAGCCACCTATCACTTTGTTTCT
44189273 TGATCAGATAAGTGTAGCC
1 TGATCAGATAAGTGTAGCC
44189292 GAAGCTATCA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 55 1.00
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.37
Consensus pattern (37 bp):
TGATCAGATAAGTGTAGCCACCTATCACTTTGTTTCT
Found at i:44189333 original size:52 final size:52
Alignment explanation
Indices: 44189271--44189430 Score: 196
Period size: 52 Copynumber: 2.9 Consensus size: 52
44189261 CACTTTGTTT
44189271 CTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTTCACTTGTCA
1 CTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTTCACTTGTCA
44189323 CTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTCCACTTTCCACTTGTCA
1 CTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCAC--T----TTT-CACTTGTCA
*** * *
44189382 CTTGATCAGATAACACTAG-CTAAGCTACCACTTATCACTTTGTCACTTG
1 CTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTT-TCACTTG
44189431 ATCAGAAGTA
Statistics
Matches: 95, Mismatches: 5, Indels: 16
0.82 0.04 0.14
Matches are distributed among these distances:
52 47 0.49
53 1 0.01
54 1 0.01
56 1 0.01
58 20 0.21
59 25 0.26
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.34
Consensus pattern (52 bp):
CTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTTCACTTGTCA
Found at i:44189429 original size:59 final size:59
Alignment explanation
Indices: 44189297--44189429 Score: 178
Period size: 59 Copynumber: 2.3 Consensus size: 59
44189287 TAGCCGAAGC
* * *** *
44189297 TATCACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
1 TATCACTTTTCACTTTCCACTTGTCACTTGATCAGATAACACTAGCCGAAGCTACCACT
* *
44189356 TATCACTTTCCACTTTCCACTTGTCACTTGATCAGATAACACTAG-CTAAGCTACCACT
1 TATCACTTTTCACTTTCCACTTGTCACTTGATCAGATAACACTAGCCGAAGCTACCACT
44189414 TATCACTTTGTCACTT
1 TATCACTTT-TCACTT
44189430 GATCAGAAGT
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
58 20 0.31
59 44 0.69
ACGTcount: A:0.26, C:0.27, G:0.11, T:0.36
Consensus pattern (59 bp):
TATCACTTTTCACTTTCCACTTGTCACTTGATCAGATAACACTAGCCGAAGCTACCACT
Found at i:44191820 original size:6 final size:6
Alignment explanation
Indices: 44191809--44191845 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
44191799 TTTGTCAAAG
44191809 GATTTT GATTTT GATTTT GATTTT GATTTT GATTTT G
1 GATTTT GATTTT GATTTT GATTTT GATTTT GATTTT G
44191846 TTGGATCATC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.16, C:0.00, G:0.19, T:0.65
Consensus pattern (6 bp):
GATTTT
Found at i:44215857 original size:73 final size:72
Alignment explanation
Indices: 44215773--44215941 Score: 171
Period size: 73 Copynumber: 2.3 Consensus size: 72
44215763 CCGGGCTGTA
* * * * * *
44215773 TAATAGGAAGCTCATAAGAGCCATATTTAGA-AAGCTT-ATGTGAGCCAATAACGGGTAGCTCTG
1 TAATAGGAAGCTCAAAAGAGCCAGATATAGAGAAG-TTCAAGCGAGCC-ATAACGGGAAGCTCTG
44215836 AAGAGCCAT
64 AAGAGCCAT
** * * * *
44215845 TAATCAGGAAGCTCCGAATAGCCAGATATCGAGAAGTTCAAGCGAGCCATATCGGGAAGCTCTGG
1 TAAT-AGGAAGCTCAAAAGAGCCAGATATAGAGAAGTTCAAGCGAGCCATAACGGGAAGCTCTGA
44215910 AGAGCCAT
65 AGAGCCAT
44215918 TAATTAGGAAGCTCACAAAGAGCC
1 TAA-TAGGAAGCTCA-AAAGAGCC
44215942 TTTAATTGGG
Statistics
Matches: 78, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
72 4 0.05
73 57 0.73
74 17 0.22
ACGTcount: A:0.36, C:0.20, G:0.25, T:0.20
Consensus pattern (72 bp):
TAATAGGAAGCTCAAAAGAGCCAGATATAGAGAAGTTCAAGCGAGCCATAACGGGAAGCTCTGAA
GAGCCAT
Found at i:44215930 original size:25 final size:26
Alignment explanation
Indices: 44215899--44215991 Score: 93
Period size: 26 Copynumber: 3.7 Consensus size: 26
44215889 AGCCATATCG
*
44215899 GGAAGCTC-TGGAGAGCCATTAATTA
1 GGAAGCTCATGAAGAGCCATTAATTA
** * *
44215924 GGAAGCTCACAAAGAGCCTTTAATTG
1 GGAAGCTCATGAAGAGCCATTAATTA
*
44215950 GGAAGCTCATGAAGAGCC-GTATATTA
1 GGAAGCTCATGAAGAGCCATTA-ATTA
*
44215976 GGACGCTCAT-AAGAGC
1 GGAAGCTCATGAAGAGC
44215992 TGCGGTGTGT
Statistics
Matches: 56, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
25 16 0.29
26 40 0.71
ACGTcount: A:0.33, C:0.18, G:0.27, T:0.22
Consensus pattern (26 bp):
GGAAGCTCATGAAGAGCCATTAATTA
Found at i:44216374 original size:21 final size:21
Alignment explanation
Indices: 44216350--44216389 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
44216340 GTAAATTTAG
*
44216350 CTCAATTTAATACAATTCATA
1 CTCAATTCAATACAATTCATA
*
44216371 CTCAATTCAATCCAATTCA
1 CTCAATTCAATACAATTCA
44216390 CATCTTAGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.40, C:0.25, G:0.00, T:0.35
Consensus pattern (21 bp):
CTCAATTCAATACAATTCATA
Found at i:44218022 original size:21 final size:22
Alignment explanation
Indices: 44217998--44218046 Score: 91
Period size: 21 Copynumber: 2.3 Consensus size: 22
44217988 ACCTAGTTGT
44217998 TACCTAAATTTGTACAAAAA-G
1 TACCTAAATTTGTACAAAAAGG
44218019 TACCTAAATTTGTACAAAAAGG
1 TACCTAAATTTGTACAAAAAGG
44218041 TACCTA
1 TACCTA
44218047 GTTACCTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 20 0.74
22 7 0.26
ACGTcount: A:0.45, C:0.16, G:0.10, T:0.29
Consensus pattern (22 bp):
TACCTAAATTTGTACAAAAAGG
Found at i:44224811 original size:26 final size:26
Alignment explanation
Indices: 44224782--44224832 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
44224772 GCCAAAAGTT
44224782 CTAATTGTACATGAAACCCAAATTTA
1 CTAATTGTACATGAAACCCAAATTTA
*
44224808 CTAATTGTACATGAAACTCAAATTT
1 CTAATTGTACATGAAACCCAAATTT
44224833 CTTTTCATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.41, C:0.18, G:0.08, T:0.33
Consensus pattern (26 bp):
CTAATTGTACATGAAACCCAAATTTA
Found at i:44236258 original size:28 final size:27
Alignment explanation
Indices: 44236220--44236295 Score: 73
Period size: 28 Copynumber: 2.7 Consensus size: 27
44236210 CTTTCTTTCT
44236220 AAATTCTTAATCTTCAATTTTCAATC-CC
1 AAATT-TTAAT-TTCAATTTTCAATCTCC
* * *
44236248 CAATTTCTAATTTTATATTTTCAATCTCT
1 AAATTT-TAATTTCA-ATTTTCAATCTCC
44236277 AAATTTTAATTTTCAATTT
1 AAATTTTAA-TTTCAATTT
44236296 CGAATTTTCA
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
27 4 0.10
28 25 0.64
29 10 0.26
ACGTcount: A:0.32, C:0.17, G:0.00, T:0.51
Consensus pattern (27 bp):
AAATTTTAATTTCAATTTTCAATCTCC
Found at i:44236272 original size:21 final size:20
Alignment explanation
Indices: 44236248--44236303 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 20
44236238 TTTCAATCCC
44236248 CAATTTCTAATTTTATATTTT
1 CAATTTCTAATTTTA-ATTTT
*
44236269 CAATCTCTAAATTTTAATTTT
1 CAATTTCT-AATTTTAATTTT
*
44236290 CAATTTCGAATTTT
1 CAATTTCTAATTTT
44236304 CAATCCTCAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 6 0.19
21 18 0.58
22 7 0.23
ACGTcount: A:0.30, C:0.12, G:0.02, T:0.55
Consensus pattern (20 bp):
CAATTTCTAATTTTAATTTT
Found at i:44236295 original size:35 final size:36
Alignment explanation
Indices: 44236251--44236324 Score: 84
Period size: 35 Copynumber: 2.1 Consensus size: 36
44236241 CAATCCCCAA
*
44236251 TTTCTAATTT-TATATTTTCAAT-CTCTAAAT-TTTAAT
1 TTTCTAATTTCGA-ATTTTCAATCCTC-AAATATTT-AT
44236287 TTTC-AATTTCGAATTTTCAATCCTCAAATATTTAT
1 TTTCTAATTTCGAATTTTCAATCCTCAAATATTTAT
44236322 TTT
1 TTT
44236325 AATATTTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
35 23 0.68
36 11 0.32
ACGTcount: A:0.30, C:0.14, G:0.01, T:0.55
Consensus pattern (36 bp):
TTTCTAATTTCGAATTTTCAATCCTCAAATATTTAT
Found at i:44236313 original size:21 final size:20
Alignment explanation
Indices: 44236235--44236313 Score: 50
Period size: 21 Copynumber: 3.8 Consensus size: 20
44236225 CTTAATCTTC
* *
44236235 AATTTTCAATCCCCAATTTCT
1 AATTTT-AATCCTCAATTTCA
** *
44236256 AATTTTATATTTTCAATCTCTA
1 AATTTTA-ATCCTCAATTTC-A
** *
44236278 AATTTTAATTTTCAATTTCG
1 AATTTTAATCCTCAATTTCA
44236298 AATTTTCAATCCTCAA
1 AATTTT-AATCCTCAA
44236314 ATATTTATTT
Statistics
Matches: 46, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
20 7 0.15
21 32 0.70
22 7 0.15
ACGTcount: A:0.32, C:0.19, G:0.01, T:0.48
Consensus pattern (20 bp):
AATTTTAATCCTCAATTTCA
Found at i:44237923 original size:20 final size:20
Alignment explanation
Indices: 44237900--44237938 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
44237890 GTCCAATATA
44237900 TTAAAAAGTTTACCAAAATT
1 TTAAAAAGTTTACCAAAATT
** *
44237920 TTAAAGGGTTTATCAAAAT
1 TTAAAAAGTTTACCAAAAT
44237939 AACTAAGGAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.46, C:0.08, G:0.10, T:0.36
Consensus pattern (20 bp):
TTAAAAAGTTTACCAAAATT
Found at i:44238003 original size:20 final size:19
Alignment explanation
Indices: 44237949--44238022 Score: 58
Period size: 20 Copynumber: 3.8 Consensus size: 19
44237939 AACTAAGGAT
* * *
44237949 TTACCAAACTTTCTATTGTT
1 TTACCAAAATTTCTA-AGAT
* * *
44237969 TTACCAATATATCTAATAGT
1 TTACCAAAATTTCTAAGA-T
* *
44237989 TTATCAAATTTTCTAAGAT
1 TTACCAAAATTTCTAAGAT
44238008 TTACCAAAATTTCTA
1 TTACCAAAATTTCTA
44238023 CCCTTTTGCC
Statistics
Matches: 40, Mismatches: 13, Indels: 3
0.71 0.23 0.05
Matches are distributed among these distances:
19 14 0.35
20 26 0.65
ACGTcount: A:0.35, C:0.16, G:0.04, T:0.45
Consensus pattern (19 bp):
TTACCAAAATTTCTAAGAT
Found at i:44238149 original size:20 final size:20
Alignment explanation
Indices: 44238126--44238212 Score: 102
Period size: 20 Copynumber: 4.3 Consensus size: 20
44238116 ATTTAGGGAT
*
44238126 TTACCAAAATATCTAACAAG
1 TTACCAATATATCTAACAAG
* * *
44238146 TTACCAATATATTTAACGAT
1 TTACCAATATATCTAACAAG
* * *
44238166 TTACCAATATTTCTAAGAAC
1 TTACCAATATATCTAACAAG
44238186 TTACCAATATATCTAACAAG
1 TTACCAATATATCTAACAAG
*
44238206 TTGCCAA
1 TTACCAA
44238213 AATTTCTATC
Statistics
Matches: 54, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 54 1.00
ACGTcount: A:0.43, C:0.20, G:0.06, T:0.32
Consensus pattern (20 bp):
TTACCAATATATCTAACAAG
Found at i:44238150 original size:40 final size:40
Alignment explanation
Indices: 44238106--44238220 Score: 122
Period size: 40 Copynumber: 2.9 Consensus size: 40
44238096 TTCTATAATT
* ** *
44238106 TTACCAAAATATTTAGGGATTTACCAAAATATCTAACAAG
1 TTACCAATATATTTAACGATTTACCAAAATATCTAACAAC
* * *
44238146 TTACCAATATATTTAACGATTTACCAATATTTCTAAGAAC
1 TTACCAATATATTTAACGATTTACCAAAATATCTAACAAC
* * * * *
44238186 TTACCAATATATCTAACAAGTTGCCAAAATTTCTA
1 TTACCAATATATTTAACGATTTACCAAAATATCTA
44238221 TCTTTTTATC
Statistics
Matches: 63, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 63 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.34
Consensus pattern (40 bp):
TTACCAATATATTTAACGATTTACCAAAATATCTAACAAC
Found at i:44238234 original size:60 final size:60
Alignment explanation
Indices: 44238126--44238255 Score: 147
Period size: 60 Copynumber: 2.2 Consensus size: 60
44238116 ATTTAGGGAT
* * *
44238126 TTACCAAAATATCTAACAAGTTACCAATATATTTAACGATTTACCAATATTTCTAAGA-A
1 TTACCAATATATCTAACAAGTTACCAAAATATTTAACGATTTACCAATATTTATAAGACA
* * ** * *
44238185 CTTACCAATATATCTAACAAGTTGCCAAAAT-TTCTATCTTTTTATCAATATTTATGAGACA
1 -TTACCAATATATCTAACAAGTTACCAAAATATT-TAACGATTTACCAATATTTATAAGACA
44238246 TTACCAATAT
1 TTACCAATAT
44238256 TCCCAAATTT
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
59 2 0.03
60 56 0.95
61 1 0.02
ACGTcount: A:0.40, C:0.18, G:0.05, T:0.37
Consensus pattern (60 bp):
TTACCAATATATCTAACAAGTTACCAAAATATTTAACGATTTACCAATATTTATAAGACA
Found at i:44238356 original size:20 final size:20
Alignment explanation
Indices: 44238333--44238377 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
44238323 TTTATGAGAC
* *
44238333 TTTACCAATATTTCTAAAGA
1 TTTACCAAAATATCTAAAGA
*
44238353 TTTACCAAAATATCTAACGA
1 TTTACCAAAATATCTAAAGA
44238373 TTTAC
1 TTTAC
44238378 TGGTATATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.40, C:0.18, G:0.04, T:0.38
Consensus pattern (20 bp):
TTTACCAAAATATCTAAAGA
Found at i:44238455 original size:19 final size:20
Alignment explanation
Indices: 44238412--44238458 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
44238402 TTTTTAAAGT
44238412 TTTACCAAAACATCTAACAA
1 TTTACCAAAACATCTAACAA
* *
44238432 TTTACTAAAATATCTAAC-A
1 TTTACCAAAACATCTAACAA
44238451 TTTACCAA
1 TTTACCAA
44238459 TATTTATGAG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.47, C:0.21, G:0.00, T:0.32
Consensus pattern (20 bp):
TTTACCAAAACATCTAACAA
Found at i:44238497 original size:20 final size:19
Alignment explanation
Indices: 44238474--44238512 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
44238464 ATGAGACTTA
44238474 ACCAAAATTTCCAACATTTT
1 ACCAAAATTTCCAA-ATTTT
* *
44238494 ACCAATATTTTCAAATTTT
1 ACCAAAATTTCCAAATTTT
44238513 CTAAACCCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.38, C:0.21, G:0.00, T:0.41
Consensus pattern (19 bp):
ACCAAAATTTCCAAATTTT
Found at i:44238633 original size:20 final size:20
Alignment explanation
Indices: 44238560--44238634 Score: 62
Period size: 20 Copynumber: 3.8 Consensus size: 20
44238550 TCTATAAATA
* **
44238560 TACCAAAATATCTATGGATTT
1 TACCAATATATCTAAAGA-TT
* **
44238581 TA-CAATATATCGAACTATT
1 TACCAATATATCTAAAGATT
* *
44238600 TCCCAATATTTCTAAAGATT
1 TACCAATATATCTAAAGATT
44238620 TACCAATATATCTAA
1 TACCAATATATCTAA
44238635 CGACCAAAAT
Statistics
Matches: 41, Mismatches: 12, Indels: 3
0.73 0.21 0.05
Matches are distributed among these distances:
19 3 0.07
20 36 0.88
21 2 0.05
ACGTcount: A:0.40, C:0.17, G:0.05, T:0.37
Consensus pattern (20 bp):
TACCAATATATCTAAAGATT
Done.