Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold60
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: 3815296
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 18690 characters in sequence are not A, C, G, or T
File 17 of 21
Found at i:2753389 original size:2 final size:2
Alignment explanation
Indices: 2753382--2753420 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2753372 GAATATAAGG
2753382 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2753421 GAAAACAAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2753787 original size:2 final size:2
Alignment explanation
Indices: 2753780--2753809 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2753770 CTTCTTAGCA
*
2753780 TC TC TC TC TC TC TC TC TC CC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
2753810 GCTCGCTCGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
TC
Found at i:2755421 original size:2 final size:2
Alignment explanation
Indices: 2755414--2755450 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
2755404 CTTCAACAAC
*
2755414 AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2755451 CCTCCATAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2762214 original size:5 final size:5
Alignment explanation
Indices: 2762206--2762234 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
2762196 CTTTTCTCCC
2762206 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
2762235 TGTTGTAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:2762645 original size:15 final size:14
Alignment explanation
Indices: 2762625--2762668 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
2762615 TTAAATTTAG
2762625 ATTTAATATAATAAT
1 ATTTAATAT-ATAAT
*
2762640 ATTTAATAT-TTAT
1 ATTTAATATATAAT
2762653 ATTTAATATATTAAT
1 ATTTAATATA-TAAT
2762668 A
1 A
2762669 ATGTATATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
13 12 0.48
15 13 0.52
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
ATTTAATATATAAT
Found at i:2762657 original size:28 final size:29
Alignment explanation
Indices: 2762615--2762684 Score: 90
Period size: 28 Copynumber: 2.4 Consensus size: 29
2762605 ATTATTATTA
*
2762615 TTAA-ATTTAGATTTAATATAATAAT-AT
1 TTAATATTTATATTTAATATAATAATAAT
*
2762642 TTAATATTTATATTTAATATATTAATAAT
1 TTAATATTTATATTTAATATAATAATAAT
*
2762671 GTATATATTTATAT
1 TTA-ATATTTATAT
2762685 ATTTATACAT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
27 4 0.11
28 19 0.51
29 4 0.11
30 10 0.27
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (29 bp):
TTAATATTTATATTTAATATAATAATAAT
Found at i:2762668 original size:8 final size:8
Alignment explanation
Indices: 2762627--2762708 Score: 59
Period size: 8 Copynumber: 10.5 Consensus size: 8
2762617 AAATTTAGAT
2762627 TTAATATA
1 TTAATATA
*
2762635 ATAATAT-
1 TTAATATA
2762642 TTAATAT-
1 TTAATATA
2762649 TT-ATAT-
1 TTAATATA
2762655 TTAATATA
1 TTAATATA
2762663 TTAATA-A
1 TTAATATA
2762670 TGT-ATATA
1 T-TAATATA
*
2762678 TTTATATA
1 TTAATATA
*
2762686 TTTATACATTA
1 -TTA-ATA-TA
2762697 TTAATATA
1 TTAATATA
2762705 TTAA
1 TTAA
2762709 AAGGTTATAT
Statistics
Matches: 61, Mismatches: 5, Indels: 16
0.74 0.06 0.20
Matches are distributed among these distances:
6 6 0.10
7 18 0.30
8 26 0.43
9 4 0.07
10 5 0.08
11 2 0.03
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (8 bp):
TTAATATA
Found at i:2763619 original size:27 final size:27
Alignment explanation
Indices: 2763542--2763622 Score: 85
Period size: 27 Copynumber: 3.0 Consensus size: 27
2763532 AAATAAAAAT
* *
2763542 ATTTGATTAATATAATATTTTTATTA-A
1 ATTT-ATTAAAATAATATTTTAATTATA
**
2763569 ATTTAATTAAAATAATATACTAATTATA
1 ATTT-ATTAAAATAATATTTTAATTATA
2763597 TATTT-TTAAAATAATATTTTAATTAT
1 -ATTTATTAAAATAATATTTTAATTAT
2763623 TTTTAATTGA
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
27 40 0.89
28 1 0.02
29 4 0.09
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (27 bp):
ATTTATTAAAATAATATTTTAATTATA
Found at i:2763942 original size:2 final size:2
Alignment explanation
Indices: 2763935--2763969 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
2763925 CACTTTCTTT
*
2763935 TA TA TA TA TA TA TA TA TA TA TA TA GA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2763970 CTTTTAAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2764727 original size:6 final size:6
Alignment explanation
Indices: 2764722--2764756 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
2764712 AAAAAGATGA
*
2764722 AAATGA AAATGC AAATGC AAATGC AAATGC AAATG
1 AAATGC AAATGC AAATGC AAATGC AAATGC AAATG
2764757 ATTAATTACC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.54, C:0.11, G:0.17, T:0.17
Consensus pattern (6 bp):
AAATGC
Found at i:2764737 original size:12 final size:12
Alignment explanation
Indices: 2764718--2764757 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
2764708 AAAAAAAAAG
*
2764718 ATGAAAATGAAA
1 ATGAAAATGCAA
*
2764730 ATGCAAATGCAA
1 ATGAAAATGCAA
*
2764742 ATGCAAATGCAA
1 ATGAAAATGCAA
2764754 ATGA
1 ATGA
2764758 TTAATTACCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.55, C:0.10, G:0.17, T:0.17
Consensus pattern (12 bp):
ATGAAAATGCAA
Found at i:2764743 original size:18 final size:18
Alignment explanation
Indices: 2764718--2764757 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
2764708 AAAAAAAAAG
2764718 ATGAAAATGAAAATGCAA
1 ATGAAAATGAAAATGCAA
* *
2764736 ATGCAAATGCAAATGCAA
1 ATGAAAATGAAAATGCAA
2764754 ATGA
1 ATGA
2764758 TTAATTACCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.55, C:0.10, G:0.17, T:0.17
Consensus pattern (18 bp):
ATGAAAATGAAAATGCAA
Found at i:2767856 original size:26 final size:26
Alignment explanation
Indices: 2767807--2767858 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
2767797 TAAATGTAAA
* *
2767807 TTAAATAAAATATCGAATATAAATAT
1 TTAAATAAAATATCGAAAACAAATAT
2767833 TTAAATAAAAATATC-AAAACAAATAT
1 TTAAAT-AAAATATCGAAAACAAATAT
2767859 ATATATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 15 0.65
27 8 0.35
ACGTcount: A:0.62, C:0.06, G:0.02, T:0.31
Consensus pattern (26 bp):
TTAAATAAAATATCGAAAACAAATAT
Found at i:2769487 original size:5 final size:5
Alignment explanation
Indices: 2769472--2769528 Score: 53
Period size: 5 Copynumber: 11.0 Consensus size: 5
2769462 AAACATAATT
* * *
2769472 ATATAA ATATA ATATA AT-TA AAATA ATTAAA ATATA ATATG ATATA ATATAA
1 ATAT-A ATATA ATATA ATATA ATATA A-TATA ATATA ATATA ATATA ATAT-A
2769524 ATATA
1 ATATA
2769529 TATTTTAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
4 3 0.07
5 27 0.64
6 12 0.29
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (5 bp):
ATATA
Found at i:2769572 original size:17 final size:18
Alignment explanation
Indices: 2769550--2769583 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2769540 TTATATAATA
*
2769550 TAAATTATTA-AAATATT
1 TAAATTAATATAAATATT
2769567 TAAATTAATATAAATAT
1 TAAATTAATATAAATAT
2769584 AAAATATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TAAATTAATATAAATATT
Found at i:2769602 original size:27 final size:28
Alignment explanation
Indices: 2769542--2769602 Score: 92
Period size: 27 Copynumber: 2.2 Consensus size: 28
2769532 TTTAAAATTT
2769542 ATATAATATAAATTATTAAAATATTTAA
1 ATATAATATAAATTATTAAAATATTTAA
2769570 AT-TAATATAAA-TA-TAAAATATTTTAA
1 ATATAATATAAATTATTAAAATA-TTTAA
2769596 ATATAAT
1 ATATAAT
2769603 TATTATATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
25 7 0.23
26 9 0.29
27 13 0.42
28 2 0.06
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (28 bp):
ATATAATATAAATTATTAAAATATTTAA
Found at i:2769609 original size:25 final size:23
Alignment explanation
Indices: 2769475--2769609 Score: 93
Period size: 25 Copynumber: 5.7 Consensus size: 23
2769465 CATAATTATA
*
2769475 TAAATATAATATAATTAAAATAATT
1 TAAATATAATATTA-TAAAAT-ATT
* * *
2769500 AAAATATAATATGATATAATA--
1 TAAATATAATATTATAAAATATT
*
2769521 TAAATAT-ATATTTTAAAAT-TT
1 TAAATATAATATTATAAAATATT
2769542 ATATAATATAA-ATTATTAAAATATT
1 -TA-AATATAATATTA-TAAAATATT
2769567 TAAAT-TAATATAAATATAAAATATTT
1 TAAATATAATAT---TATAAAATA-TT
2769593 TAAATATAATTATTATA
1 TAAATATAA-TATTATA
2769610 TAACAAAAAT
Statistics
Matches: 88, Mismatches: 8, Indels: 28
0.71 0.06 0.23
Matches are distributed among these distances:
20 9 0.10
21 6 0.07
22 5 0.06
23 14 0.16
24 14 0.16
25 25 0.28
26 9 0.10
27 3 0.03
28 3 0.03
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (23 bp):
TAAATATAATATTATAAAATATT
Found at i:2772429 original size:15 final size:15
Alignment explanation
Indices: 2772405--2772436 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2772395 CGTGGGGCTT
*
2772405 AAGAATAGAAAAAGA
1 AAGAAAAGAAAAAGA
2772420 AAGAAAAGAAAAAGA
1 AAGAAAAGAAAAAGA
2772435 AA
1 AA
2772437 AGTACTTAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.03
Consensus pattern (15 bp):
AAGAAAAGAAAAAGA
Found at i:2774489 original size:2 final size:2
Alignment explanation
Indices: 2774482--2774518 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2774472 TATGTTTGTG
2774482 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2774519 ATGGTGGTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2775445 original size:13 final size:13
Alignment explanation
Indices: 2775427--2775455 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
2775417 TCCCCCATCC
2775427 CTTTGTCATGACT
1 CTTTGTCATGACT
2775440 CTTTGTCATGACT
1 CTTTGTCATGACT
2775453 CTT
1 CTT
2775456 AATCTACCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.14, C:0.24, G:0.14, T:0.48
Consensus pattern (13 bp):
CTTTGTCATGACT
Found at i:2778024 original size:21 final size:21
Alignment explanation
Indices: 2777999--2778039 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2777989 AAAAATTATT
2777999 TAAAT-TTAATTATAAAATAAA
1 TAAATATTAATT-TAAAATAAA
2778020 TAAATATTAATTTAAAATAA
1 TAAATATTAATTTAAAATAA
2778040 TATTTTAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
TAAATATTAATTTAAAATAAA
Found at i:2778542 original size:2 final size:2
Alignment explanation
Indices: 2778535--2778564 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2778525 GATTTTAGTC
2778535 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
2778565 TAAAAAGAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2779945 original size:23 final size:24
Alignment explanation
Indices: 2779900--2779945 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
2779890 ATCCTGCAGT
*
2779900 ACTTCCTTCGCTTCTCCTTCAACC
1 ACTTCCTTCGCTTCTCATTCAACC
2779924 ACTT-CTTCG-TTCTCATTGCAAC
1 ACTTCCTTCGCTTCTCATT-CAAC
2779946 AACATTGCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 7 0.35
23 9 0.45
24 4 0.20
ACGTcount: A:0.15, C:0.39, G:0.07, T:0.39
Consensus pattern (24 bp):
ACTTCCTTCGCTTCTCATTCAACC
Found at i:2781676 original size:19 final size:19
Alignment explanation
Indices: 2781648--2781693 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
2781638 TACTTTTTAA
*
2781648 ATTAAGAAAAAAT-TATATT
1 ATTAATAAAAAATAT-TATT
2781667 ATTAATAAAAAATATTATT
1 ATTAATAAAAAATATTATT
2781686 ATT-ATAAA
1 ATTAATAAA
2781694 TATAATAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 5 0.20
19 19 0.76
20 1 0.04
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (19 bp):
ATTAATAAAAAATATTATT
Found at i:2781686 original size:24 final size:25
Alignment explanation
Indices: 2781660--2781747 Score: 83
Period size: 27 Copynumber: 3.5 Consensus size: 25
2781650 TAAGAAAAAA
*
2781660 TTATATTATTAATA-AAAAATA-TT
1 TTATATTATAAATATAAAAATAGTT
* *
2781683 AT-TATTATAAATATAATAATAGTTT
1 TTATATTATAAATATAAAAATAG-TT
*
2781708 TTATTATTATAAATATAATAATAGTTT
1 TTA-TATTATAAATATAAAAATAG-TT
2781735 TTATTATTATAAA
1 TTA-TATTATAAA
2781748 AATTATTTTA
Statistics
Matches: 56, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
22 10 0.18
23 7 0.12
25 3 0.05
27 36 0.64
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (25 bp):
TTATATTATAAATATAAAAATAGTT
Found at i:2781699 original size:27 final size:27
Alignment explanation
Indices: 2781681--2781747 Score: 134
Period size: 27 Copynumber: 2.5 Consensus size: 27
2781671 ATAAAAAATA
2781681 TTATTATTATAAATATAATAATAGTTT
1 TTATTATTATAAATATAATAATAGTTT
2781708 TTATTATTATAAATATAATAATAGTTT
1 TTATTATTATAAATATAATAATAGTTT
2781735 TTATTATTATAAA
1 TTATTATTATAAA
2781748 AATTATTTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (27 bp):
TTATTATTATAAATATAATAATAGTTT
Found at i:2781756 original size:21 final size:21
Alignment explanation
Indices: 2781655--2781756 Score: 55
Period size: 21 Copynumber: 4.6 Consensus size: 21
2781645 TAAATTAAGA
* *
2781655 AAAAATTA-TATTATTAATAA
1 AAAAATTATTTTTATTAATAT
* *
2781675 AAAATATTATTATTATAAATAT
1 AAAA-ATTATTTTTATTAATAT
* *
2781697 AATAA-TAGTTTTTATTATTAT
1 AAAAATTA-TTTTTATTAATAT
*
2781718 AAATATAATAATAGTTTTTATTATTAT
1 -AA-A-AAT--TA-TTTTTATTAATAT
2781745 AAAAATTATTTT
1 AAAAATTATTTT
2781757 ATTTATGATT
Statistics
Matches: 66, Mismatches: 7, Indels: 17
0.73 0.08 0.19
Matches are distributed among these distances:
20 6 0.09
21 19 0.29
22 17 0.26
24 5 0.08
25 1 0.02
26 2 0.03
27 16 0.24
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (21 bp):
AAAAATTATTTTTATTAATAT
Found at i:2781794 original size:14 final size:13
Alignment explanation
Indices: 2781775--2781847 Score: 55
Period size: 14 Copynumber: 5.6 Consensus size: 13
2781765 TTAATAATAA
2781775 TAAATTTATTTATT
1 TAAA-TTATTTATT
*
2781789 TAAATTA-TAATCT
1 TAAATTATTTAT-T
2781802 TATAATTA--T-TT
1 TA-AATTATTTATT
*
2781813 TAAATAATTTATT
1 TAAATTATTTATT
*
2781826 TAATTTATTTAATT
1 TAAATTATTT-ATT
2781840 TAAATTAT
1 TAAATTAT
2781848 AATCATCTAA
Statistics
Matches: 47, Mismatches: 6, Indels: 12
0.72 0.09 0.18
Matches are distributed among these distances:
10 4 0.09
11 3 0.06
12 5 0.11
13 16 0.34
14 19 0.40
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (13 bp):
TAAATTATTTATT
Found at i:2781829 original size:9 final size:9
Alignment explanation
Indices: 2781817--2781841 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
2781807 TTATTTTAAA
2781817 TAATTTATT
1 TAATTTATT
2781826 TAATTTATT
1 TAATTTATT
2781835 TAATTTA
1 TAATTTA
2781842 AATTATAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (9 bp):
TAATTTATT
Found at i:2781895 original size:39 final size:42
Alignment explanation
Indices: 2781841--2781935 Score: 124
Period size: 44 Copynumber: 2.3 Consensus size: 42
2781831 TATTTAATTT
* *
2781841 AAATTATAATCATCTAATTA-TTT-TCT-AAATTTGAATTAA
1 AAATTATAATAATCTAATTATTTTATCTCAAATTTAAATTAA
*
2781880 AAATTATAATAATCTAATTATTTTAAATTTCAAATTTAAATTAA
1 AAATTATAATAATCTAATTATTTT--ATCTCAAATTTAAATTAA
2781924 AAATTATAATAA
1 AAATTATAATAA
2781936 CCTCTTAATA
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
39 19 0.40
40 3 0.06
43 2 0.04
44 24 0.50
ACGTcount: A:0.49, C:0.05, G:0.01, T:0.44
Consensus pattern (42 bp):
AAATTATAATAATCTAATTATTTTATCTCAAATTTAAATTAA
Found at i:2781921 original size:37 final size:38
Alignment explanation
Indices: 2781832--2781922 Score: 116
Period size: 39 Copynumber: 2.4 Consensus size: 38
2781822 TATTTAATTT
*
2781832 ATTT-AATTTAAATTATAATCATCTAATTATTTTCTAA
1 ATTTAAATTTAAATTATAATAATCTAATTATTTTCTAA
* *
2781869 ATTTGAATTAAAAATTATAATAATCTAATTA-TTT-TAA
1 ATTTAAATT-TAAATTATAATAATCTAATTATTTTCTAA
2781906 ATTTCAAATTTAAATTA
1 ATTT-AAATTTAAATTA
2781923 AAAATTATAA
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
37 17 0.36
38 11 0.23
39 19 0.40
ACGTcount: A:0.45, C:0.05, G:0.01, T:0.48
Consensus pattern (38 bp):
ATTTAAATTTAAATTATAATAATCTAATTATTTTCTAA
Found at i:2781967 original size:24 final size:23
Alignment explanation
Indices: 2781940--2782012 Score: 55
Period size: 24 Copynumber: 3.2 Consensus size: 23
2781930 TAATAACCTC
2781940 TTAATAATATAATCTTTTATTAAT
1 TTAATAATATAAT-TTTTATTAAT
***
2781964 TTAA-AAT-T-ATATAAAATT-AT
1 TTAATAATATAAT-TTTTATTAAT
2781984 ATTAATAATATAATTTTATATTAAT
1 -TTAATAATATAATTTT-TATTAAT
2782009 TTAA
1 TTAA
2782013 AAAATAAAAT
Statistics
Matches: 36, Mismatches: 7, Indels: 12
0.65 0.13 0.22
Matches are distributed among these distances:
20 2 0.06
21 10 0.28
22 4 0.11
23 5 0.14
24 13 0.36
25 2 0.06
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (23 bp):
TTAATAATATAATTTTTATTAAT
Found at i:2781996 original size:19 final size:19
Alignment explanation
Indices: 2781972--2782008 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2781962 ATTTAAAATT
2781972 ATATAAAATTATATTAATA
1 ATATAAAATTATATTAATA
**
2781991 ATATAATTTTATATTAAT
1 ATATAAAATTATATTAAT
2782009 TTAAAAAATA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATATAAAATTATATTAATA
Found at i:2790173 original size:38 final size:38
Alignment explanation
Indices: 2790115--2790233 Score: 132
Period size: 38 Copynumber: 3.1 Consensus size: 38
2790105 GAAATTCCTT
* * *
2790115 AGCCACCAACAAATTCCAAATTAAATTCTCTAGCCATC
1 AGCCACCAACCAATTTCAAATTAAATTCTCTAGCCACC
** *
2790153 AGCCA-CAAGCCAATTTCAAATTAAATTCTCTAATCGCC
1 AGCCACCAA-CCAATTTCAAATTAAATTCTCTAGCCACC
* * **
2790191 AGCCACCAACCAATTTTAAATTGAATTCTCTAGCTGCC
1 AGCCACCAACCAATTTCAAATTAAATTCTCTAGCCACC
2790229 AGCCA
1 AGCCA
2790234 ATTCAATTTG
Statistics
Matches: 68, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
37 3 0.04
38 62 0.91
39 3 0.04
ACGTcount: A:0.36, C:0.30, G:0.08, T:0.25
Consensus pattern (38 bp):
AGCCACCAACCAATTTCAAATTAAATTCTCTAGCCACC
Found at i:2801433 original size:41 final size:41
Alignment explanation
Indices: 2801378--2801456 Score: 140
Period size: 41 Copynumber: 1.9 Consensus size: 41
2801368 AAACGAAAGG
* *
2801378 AAAAAAATACAATTCGTCTTCATGTCTTAATTAAGAAATAA
1 AAAAAAAAACAATTCGTCTTCATCTCTTAATTAAGAAATAA
2801419 AAAAAAAAACAATTCGTCTTCATCTCTTAATTAAGAAA
1 AAAAAAAAACAATTCGTCTTCATCTCTTAATTAAGAAA
2801457 CCCCATTCAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.49, C:0.14, G:0.06, T:0.30
Consensus pattern (41 bp):
AAAAAAAAACAATTCGTCTTCATCTCTTAATTAAGAAATAA
Found at i:2802989 original size:15 final size:14
Alignment explanation
Indices: 2802954--2802998 Score: 56
Period size: 15 Copynumber: 3.2 Consensus size: 14
2802944 CATATGGTAT
*
2802954 ATTATTTTTAATAA
1 ATTATATTTAATAA
*
2802968 ATGATATTTAATAAA
1 ATTATATTTAAT-AA
2802983 ATTATATTTAA-AA
1 ATTATATTTAATAA
2802996 ATT
1 ATT
2802999 CAGCATATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
13 5 0.19
14 10 0.37
15 12 0.44
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (14 bp):
ATTATATTTAATAA
Found at i:2804399 original size:3 final size:3
Alignment explanation
Indices: 2804391--2804422 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
2804381 CTTTCTTCAG
2804391 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
2804423 TGCAGGCTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.31, G:0.00, T:0.34
Consensus pattern (3 bp):
ATC
Found at i:2805333 original size:18 final size:18
Alignment explanation
Indices: 2805289--2805336 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
2805279 AGTAAACTCG
*
2805289 TTTTATTATTAAAATATAT
1 TTTTA-TATTAAAAAATAT
***
2805308 TAAAATATTAAAAAATAT
1 TTTTATATTAAAAAATAT
2805326 TTTTATATTAA
1 TTTTATATTAA
2805337 TATTTATATA
Statistics
Matches: 22, Mismatches: 7, Indels: 1
0.73 0.23 0.03
Matches are distributed among these distances:
18 20 0.91
19 2 0.09
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTTATATTAAAAAATAT
Found at i:2807168 original size:35 final size:36
Alignment explanation
Indices: 2807127--2807203 Score: 86
Period size: 35 Copynumber: 2.1 Consensus size: 36
2807117 TATGTAAAAT
* *
2807127 TAAAAAACCTCACAATCATTATATAC-GATAATTA-TA
1 TAAAAATCCT-ACAATCAATATAT-CTGATAATTATTA
* *
2807163 TAAAAATCCTATAATTAATATATCTGATAATTATTA
1 TAAAAATCCTACAATCAATATATCTGATAATTATTA
2807199 TAAAA
1 TAAAA
2807204 TTATGGTAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
34 1 0.03
35 18 0.51
36 16 0.46
ACGTcount: A:0.51, C:0.12, G:0.03, T:0.35
Consensus pattern (36 bp):
TAAAAATCCTACAATCAATATATCTGATAATTATTA
Found at i:2807435 original size:2 final size:2
Alignment explanation
Indices: 2807428--2807467 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
2807418 GCTTCCATCC
* *
2807428 TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TT 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
2807468 CAATCTTGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2807896 original size:40 final size:39
Alignment explanation
Indices: 2807853--2807927 Score: 98
Period size: 40 Copynumber: 1.9 Consensus size: 39
2807843 ATTTATAATT
* *
2807853 TTTTTA-ATACTTTTAATGTATAGTAGATATTATTAATAG
1 TTTTTATATACTTTTAATATATAGTAAATA-TATTAATAG
* *
2807892 TTTTTATATATTTTTAATATATATTAAATATATTAA
1 TTTTTATATACTTTTAATATATAGTAAATATATTAA
2807928 ATAATTATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 12 0.39
40 19 0.61
ACGTcount: A:0.39, C:0.01, G:0.05, T:0.55
Consensus pattern (39 bp):
TTTTTATATACTTTTAATATATAGTAAATATATTAATAG
Found at i:2807922 original size:20 final size:20
Alignment explanation
Indices: 2807858--2807922 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
2807848 TAATTTTTTT
* * *
2807858 AATACTTTTAATGTATAGTA
1 AATATTTTTAATATATATTA
* * *
2807878 GATATTATTAATAGT-TTTTA
1 AATATTTTTAATA-TATATTA
*
2807898 TATATTTTTAATATATATTA
1 AATATTTTTAATATATATTA
2807918 AATAT
1 AATAT
2807923 ATTAAATAAT
Statistics
Matches: 33, Mismatches: 10, Indels: 4
0.70 0.21 0.09
Matches are distributed among these distances:
19 1 0.03
20 31 0.94
21 1 0.03
ACGTcount: A:0.40, C:0.02, G:0.06, T:0.52
Consensus pattern (20 bp):
AATATTTTTAATATATATTA
Found at i:2809238 original size:2 final size:2
Alignment explanation
Indices: 2809231--2809261 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2809221 TAATAATAAT
2809231 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2809262 GCTACTTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2809789 original size:21 final size:18
Alignment explanation
Indices: 2809752--2809796 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 18
2809742 CTATATGTCA
2809752 TATATTATTAATTAAAAT
1 TATATTATTAATTAAAAT
2809770 TATATGTATTTAATTTAAAAT
1 TATAT-TA-TTAA-TTAAAAT
*
2809791 TTTATT
1 TATATT
2809797 TTATTTATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 5 0.22
19 2 0.09
20 5 0.22
21 11 0.48
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (18 bp):
TATATTATTAATTAAAAT
Found at i:2810199 original size:22 final size:21
Alignment explanation
Indices: 2810169--2810219 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 21
2810159 ATAATATGTT
* *
2810169 TATTATTTTATTAGTATTTAAA
1 TATTTTTTTAATAGTA-TTAAA
* *
2810191 TATTTTTTTAATATTATTAAT
1 TATTTTTTTAATAGTATTAAA
2810212 TATTTTTT
1 TATTTTTT
2810220 ATTTATTATT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
21 12 0.48
22 13 0.52
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (21 bp):
TATTTTTTTAATAGTATTAAA
Found at i:2810226 original size:21 final size:21
Alignment explanation
Indices: 2810168--2810230 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 21
2810158 TATAATATGT
*
2810168 TTATTATTTTA-TTAGTATTTAA
1 TTATT-TTTTATTTATTA-TTAA
* *
2810190 ATATTTTTT-TAATATTATTAA
1 TTATTTTTTAT-TTATTATTAA
2810211 TTATTTTTTATTTATTATTA
1 TTATTTTTTATTTATTATTA
2810231 TTTAAAAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
21 24 0.73
22 9 0.27
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.67
Consensus pattern (21 bp):
TTATTTTTTATTTATTATTAA
Found at i:2810248 original size:8 final size:8
Alignment explanation
Indices: 2810230--2810287 Score: 52
Period size: 8 Copynumber: 7.5 Consensus size: 8
2810220 ATTTATTATT
2810230 ATTTAAAAA
1 ATTT-AAAA
2810239 ATTTAAAA
1 ATTTAAAA
2810247 ATTTAAAA
1 ATTTAAAA
2810255 A-TT--AA
1 ATTTAAAA
*
2810260 ATTTAATA
1 ATTTAAAA
*
2810268 ATATAAAA
1 ATTTAAAA
2810276 A-TTAAAA
1 ATTTAAAA
2810283 TATTT
1 -ATTT
2810288 TTTTATTATA
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
5 3 0.08
6 2 0.05
7 7 0.17
8 22 0.55
9 6 0.15
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (8 bp):
ATTTAAAA
Found at i:2810262 original size:21 final size:21
Alignment explanation
Indices: 2810237--2810281 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
2810227 ATTATTTAAA
*
2810237 AAATTTAAAAATTTAAAAATT
1 AAATTTAAAAATATAAAAATT
*
2810258 AAATTTAATAATATAAAAATT
1 AAATTTAAAAATATAAAAATT
2810279 AAA
1 AAA
2810282 ATATTTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
AAATTTAAAAATATAAAAATT
Found at i:2812428 original size:2 final size:2
Alignment explanation
Indices: 2812423--2812452 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2812413 GGTTTAACGA
2812423 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
2812453 GTTTTATGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2814651 original size:4 final size:4
Alignment explanation
Indices: 2814642--2814669 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
2814632 ATCTGGTATT
2814642 GACA GACA GACA GACA GACA GACA GACA
1 GACA GACA GACA GACA GACA GACA GACA
2814670 CGTGGGGGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.25, G:0.25, T:0.00
Consensus pattern (4 bp):
GACA
Found at i:2819321 original size:15 final size:16
Alignment explanation
Indices: 2819282--2819342 Score: 63
Period size: 15 Copynumber: 3.8 Consensus size: 16
2819272 TTCAATATTT
*
2819282 AAAAT-AATTTAAGTA
1 AAAATAAATTTAAATA
2819297 AAATATTAAATTTAAA-A
1 AAA-A-TAAATTTAAATA
*
2819314 AAAATAAATATAAATA
1 AAAATAAATTTAAATA
2819330 AAAATAAGATTTA
1 AAAATAA-ATTTA
2819343 TTTTATCAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
15 12 0.32
16 10 0.26
17 9 0.24
18 7 0.18
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (16 bp):
AAAATAAATTTAAATA
Found at i:2819753 original size:15 final size:14
Alignment explanation
Indices: 2819732--2819788 Score: 53
Period size: 14 Copynumber: 3.9 Consensus size: 14
2819722 TTTTATACAG
2819732 ATAAATTATGATATT
1 ATAAATTAT-ATATT
* *
2819747 TTAAATTTTTATATT
1 ATAAA-TTATATATT
*
2819762 ACAAATTATATATT
1 ATAAATTATATATT
2819776 A-AACATTATATAT
1 ATAA-ATTATATAT
2819789 ATTATATAAG
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
13 2 0.06
14 18 0.51
15 12 0.34
16 3 0.09
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.49
Consensus pattern (14 bp):
ATAAATTATATATT
Found at i:2820790 original size:24 final size:25
Alignment explanation
Indices: 2820743--2820794 Score: 72
Period size: 24 Copynumber: 2.1 Consensus size: 25
2820733 TTAATAAAAA
2820743 TAAAAATAATATAATATAATATATT
1 TAAAAATAATATAATATAATATATT
*
2820768 TAAATATAAT-TAATAT-ATCATATT
1 TAAAAATAATATAATATAAT-ATATT
2820792 TAA
1 TAA
2820795 TGCGTGTAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 2 0.08
24 14 0.56
25 9 0.36
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (25 bp):
TAAAAATAATATAATATAATATATT
Found at i:2821060 original size:1 final size:1
Alignment explanation
Indices: 2821050--2821079 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
2821040 AATCCCTCCT
*
2821050 CCCCCTCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
2821080 AATGCAATCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.97, G:0.00, T:0.03
Consensus pattern (1 bp):
C
Found at i:2822493 original size:13 final size:14
Alignment explanation
Indices: 2822470--2822499 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
2822460 TATATAAATT
2822470 TATATAAATATAAA
1 TATATAAATATAAA
2822484 TATA-AAATATAAA
1 TATATAAATATAAA
2822497 TAT
1 TAT
2822500 TTTTAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
TATATAAATATAAA
Found at i:2826011 original size:21 final size:21
Alignment explanation
Indices: 2825977--2826025 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
2825967 TTTTAATTAG
* *
2825977 ATAAAGATGAAAAAATCAT-A
1 ATAAATATGAAAAAATAATAA
2825997 ATAAATATAGAAAAAATAATAA
1 ATAAATAT-GAAAAAATAATAA
2826019 ATAAATA
1 ATAAATA
2826026 CTAATGAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 7 0.28
21 10 0.40
22 8 0.32
ACGTcount: A:0.69, C:0.02, G:0.06, T:0.22
Consensus pattern (21 bp):
ATAAATATGAAAAAATAATAA
Found at i:2826234 original size:20 final size:19
Alignment explanation
Indices: 2826211--2826258 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 19
2826201 TTAAAGTTGG
2826211 TTAATATAATATTT-ATAATA
1 TTAA-ATAATATTTGAT-ATA
*
2826231 TTAAAATTATATTTGATATA
1 TT-AAATAATATTTGATATA
2826251 TTAAATAA
1 TTAAATAA
2826259 AGATGTTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
19 5 0.21
20 15 0.62
21 4 0.17
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (19 bp):
TTAAATAATATTTGATATA
Found at i:2826656 original size:25 final size:27
Alignment explanation
Indices: 2826628--2826677 Score: 77
Period size: 25 Copynumber: 1.9 Consensus size: 27
2826618 AAAATTTTGA
2826628 TATATTTAAT-AATTAAT-ATAATATT
1 TATATTTAATCAATTAATAATAATATT
*
2826653 TATATTTAATCGATTAATAATAATA
1 TATATTTAATCAATTAATAATAATA
2826678 AAAAAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 10 0.45
26 6 0.27
27 6 0.27
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (27 bp):
TATATTTAATCAATTAATAATAATATT
Found at i:2828598 original size:25 final size:26
Alignment explanation
Indices: 2828570--2828633 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 26
2828560 TTTATATTTG
*
2828570 ATAAATATTTTTATAA-ATATAAAAT
1 ATAAATATTTTTATAATATATAAAAA
*
2828595 AT-AAT-TTTTTA-AATATTTAAAAA
1 ATAAATATTTTTATAATATATAAAAA
*
2828618 ATTAAATATATTTATA
1 A-TAAATATTTTTATA
2828634 TTTATTTAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
22 2 0.06
23 14 0.45
24 4 0.13
25 5 0.16
26 5 0.16
27 1 0.03
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (26 bp):
ATAAATATTTTTATAATATATAAAAA
Found at i:2829104 original size:26 final size:26
Alignment explanation
Indices: 2829057--2829110 Score: 65
Period size: 27 Copynumber: 2.1 Consensus size: 26
2829047 AAAAATTATT
***
2829057 AAAAATATTTTTATATTTATTTTATAA
1 AAAAATATTTTTATAAAAATTTTA-AA
2829084 AAAAATATTTTT-TAAAAATTTTAAA
1 AAAAATATTTTTATAAAAATTTTAAA
2829109 AA
1 AA
2829111 TAAAAACTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 4 0.17
26 8 0.33
27 12 0.50
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (26 bp):
AAAAATATTTTTATAAAAATTTTAAA
Found at i:2829742 original size:24 final size:23
Alignment explanation
Indices: 2829702--2829746 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
2829692 TTTAGTTATT
2829702 TTTAAAATATAATTTTTTAATAAA
1 TTTAAAATATAA-TTTTTAATAAA
*
2829726 TTTAAAATTTTAA-TTTTAATA
1 TTTAAAA-TATAATTTTTAATA
2829747 TTTATATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 8 0.42
24 7 0.37
25 4 0.21
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
TTTAAAATATAATTTTTAATAAA
Found at i:2832238 original size:13 final size:13
Alignment explanation
Indices: 2832216--2832251 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
2832206 AGAGGAGAGA
2832216 GGAAGAGGGAAGGG
1 GGAAG-GGGAAGGG
2832230 GGAAGGGGAAGGG
1 GGAAGGGGAAGGG
*
2832243 GGAGGGGGA
1 GGAAGGGGA
2832252 GGGACTCTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 16 0.76
14 5 0.24
ACGTcount: A:0.31, C:0.00, G:0.69, T:0.00
Consensus pattern (13 bp):
GGAAGGGGAAGGG
Found at i:2833320 original size:2 final size:2
Alignment explanation
Indices: 2833313--2833347 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2833303 CAGCTGGGGA
2833313 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2833348 CACAAAATCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2837212 original size:2 final size:2
Alignment explanation
Indices: 2837207--2837233 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2837197 TATATATATA
2837207 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
2837234 TCAAGGAGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:2837705 original size:20 final size:20
Alignment explanation
Indices: 2837682--2837721 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
2837672 AATTTTAAAA
* *
2837682 AAATTTAAATATATTTGTAT
1 AAATGTAAATATATTAGTAT
*
2837702 AAATGTATATATATTAGTAT
1 AAATGTAAATATATTAGTAT
2837722 CTAATATTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.47
Consensus pattern (20 bp):
AAATGTAAATATATTAGTAT
Found at i:2844539 original size:1 final size:1
Alignment explanation
Indices: 2844529--2844558 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
2844519 CAATTGGCCG
*
2844529 CCCCCACCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
2844559 AAAAAAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.03, C:0.97, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:2844999 original size:7 final size:7
Alignment explanation
Indices: 2844975--2845011 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
2844965 TTACTTAAAC
2844975 TTGTGAA
1 TTGTGAA
* *
2844982 ATGTAAA
1 TTGTGAA
2844989 TTGTGAA
1 TTGTGAA
2844996 TTGTGAA
1 TTGTGAA
2845003 TTGTGAA
1 TTGTGAA
2845010 TT
1 TT
2845012 TTTAGAAGTG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.32, C:0.00, G:0.24, T:0.43
Consensus pattern (7 bp):
TTGTGAA
Found at i:2845010 original size:14 final size:14
Alignment explanation
Indices: 2844970--2845011 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
2844960 TTAAATTACT
*
2844970 TAAACTTGTGAAATG
1 TAAA-TTGTGAATTG
2844985 TAAATTGTGAATTG
1 TAAATTGTGAATTG
*
2844999 TGAATTGTGAATT
1 TAAATTGTGAATT
2845012 TTTAGAAGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 21 0.84
15 4 0.16
ACGTcount: A:0.36, C:0.02, G:0.21, T:0.40
Consensus pattern (14 bp):
TAAATTGTGAATTG
Found at i:2848369 original size:6 final size:6
Alignment explanation
Indices: 2848360--2848391 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
2848350 ATGAAGATGG
*
2848360 GGAAAA GGAAAA AGAAAA GGAAAA GGAAAA GG
1 GGAAAA GGAAAA GGAAAA GGAAAA GGAAAA GG
2848392 GGGAAATTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (6 bp):
GGAAAA
Found at i:2849166 original size:13 final size:14
Alignment explanation
Indices: 2849134--2849167 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
2849124 GAATTTTTTT
2849134 TTTTATATATGTAA
1 TTTTATATATGTAA
2849148 TGTTTATATAT-TAA
1 T-TTTATATATGTAA
2849162 TTTTAT
1 TTTTAT
2849168 GGATCTGATG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 5 0.26
14 5 0.26
15 9 0.47
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (14 bp):
TTTTATATATGTAA
Found at i:2850099 original size:3 final size:3
Alignment explanation
Indices: 2850091--2850120 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
2850081 CTACCCATTT
2850091 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2850121 ATAACTTAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2854517 original size:2 final size:2
Alignment explanation
Indices: 2854510--2854537 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2854500 ACAATTTCAG
2854510 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
2854538 TTAAAAGCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2855930 original size:195 final size:198
Alignment explanation
Indices: 2855671--2856041 Score: 560
Period size: 195 Copynumber: 1.9 Consensus size: 198
2855661 AAAGATTTTT
2855671 TATTTTTTATTTAAAAAACCATCACTTTTCCTTAAATTTTAATATATTATTTTAAAAAAACAAAT
1 TATTTTTTATTTAAAAAACCATCACTTTTCCTTAAATTTTAATATATTATTTTAAAAAAACAAAT
2855736 TAAAAATTTTTAC-TTTT-T-CATGCTTACAA-TATTTAAAATATCAATA-AAAAAT-ATATAAA
66 TAAAAATTTTTACTTTTTATACATGCTTA-AATTATTTAAAATATCAATATAAAAATGATATAAA
*
2855795 TATA-ATATAAATATATAAATTATTTATTTATATATTTATATAAATACATACTATATAAAATTTT
130 TATATAAATAAATA-AT-AATTATTTATTT-TATATTTATATAAATACATACTATATAAAATTTT
2855859 AAAAAAA
192 AAAAAAA
*
2855866 TATTTTTTATTTAAAAAAGTCATCACTTTTCCTTAAATTTTAATATATTA-TTTAAAAAAACAAA
1 TATTTTTTATTTAAAAAA-CCATCACTTTTCCTTAAATTTTAATATATTATTTTAAAAAAACAAA
* *
2855930 TTATAAATTTTTACTTTTTCATGAACATGCTTAAATTATTTAAAATATCAATATAAATATGATAT
65 TTAAAAATTTTTACTTTTT-AT--ACATGCTTAAATTATTTAAAATATCAATATAAAAATGATAT
**
2855995 AAATATATAAATAAATAATTTTTATTTATTTTATATTTATATAAATA
127 AAATATATAAATAAATAATAATTATTTATTTTATATTTATATAAATA
2856042 TATTACATAA
Statistics
Matches: 159, Mismatches: 6, Indels: 16
0.88 0.03 0.09
Matches are distributed among these distances:
195 45 0.28
196 34 0.21
198 1 0.01
200 2 0.01
201 41 0.26
202 15 0.09
203 13 0.08
204 8 0.05
ACGTcount: A:0.47, C:0.07, G:0.01, T:0.45
Consensus pattern (198 bp):
TATTTTTTATTTAAAAAACCATCACTTTTCCTTAAATTTTAATATATTATTTTAAAAAAACAAAT
TAAAAATTTTTACTTTTTATACATGCTTAAATTATTTAAAATATCAATATAAAAATGATATAAAT
ATATAAATAAATAATAATTATTTATTTTATATTTATATAAATACATACTATATAAAATTTTAAAA
AAA
Found at i:2861280 original size:2 final size:2
Alignment explanation
Indices: 2861273--2861302 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2861263 CGAATAGCTC
2861273 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
2861303 ATTACTATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:2863498 original size:3 final size:3
Alignment explanation
Indices: 2863490--2863514 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2863480 ACAAAATTTT
2863490 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
2863515 GGGACATAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:2865204 original size:18 final size:17
Alignment explanation
Indices: 2865160--2865210 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
2865150 ATGCAAATCG
2865160 AAATAAATTT-AATATAA
1 AAATAAATTTAAAT-TAA
*
2865177 AAATAAATTTAAATTAT
1 AAATAAATTTAAATTAA
2865194 AAATCAAATTTATAATT
1 AAAT-AAATTTA-AATT
2865211 TTTATATAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
17 16 0.53
18 10 0.33
19 4 0.13
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (17 bp):
AAATAAATTTAAATTAA
Found at i:2865585 original size:22 final size:22
Alignment explanation
Indices: 2865536--2865586 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
2865526 AATATTAATT
*
2865536 AATATTAAAATATAATTTTAAA
1 AATATTAAAATATAATTCTAAA
**
2865558 TTTATTAAAAT-TATATTCTAAA
1 AATATTAAAATATA-ATTCTAAA
2865580 AATATTA
1 AATATTA
2865587 TATAATTGAA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
21 2 0.09
22 21 0.91
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
AATATTAAAATATAATTCTAAA
Found at i:2865616 original size:62 final size:60
Alignment explanation
Indices: 2865490--2865617 Score: 152
Period size: 62 Copynumber: 2.1 Consensus size: 60
2865480 TAAGATTTAC
* * *
2865490 ATTTTAAATTTATTAATTATTTTTTAAAAGTAATTAAATATTAATTAATATTAAAATATA
1 ATTTTAAATTTATTAATTATATTCTAAAAATAATTAAATATTAATTAATATTAAAATATA
* * *
2865550 ATTTTAAATTTATTAAAATTATATTCTAAAAAT-ATTATATAATTGAATTAATA-TAAATTATG
1 ATTTTAAATTTATT--AATTATATTCTAAAAATAATTAAAT-ATT-AATTAATATTAAAATATA
2865612 ATTTTA
1 ATTTTA
2865618 TATTATATAA
Statistics
Matches: 58, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
60 14 0.24
61 6 0.10
62 30 0.52
63 8 0.14
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.49
Consensus pattern (60 bp):
ATTTTAAATTTATTAATTATATTCTAAAAATAATTAAATATTAATTAATATTAAAATATA
Found at i:2866919 original size:17 final size:17
Alignment explanation
Indices: 2866872--2866920 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 17
2866862 TATAAATAAA
2866872 ATTAATAT-TTAAAATT
1 ATTAATATATTAAAATT
* *
2866888 -TTATTTTA-TATAAATT
1 ATTAATATATTA-AAATT
2866904 ATTAATATATTAAAATT
1 ATTAATATATTAAAATT
2866921 TATATAAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 7
0.69 0.11 0.19
Matches are distributed among these distances:
15 7 0.28
16 5 0.20
17 11 0.44
18 2 0.08
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTAATATATTAAAATT
Found at i:2867196 original size:33 final size:33
Alignment explanation
Indices: 2867153--2867252 Score: 98
Period size: 34 Copynumber: 2.9 Consensus size: 33
2867143 ATTAAATTTA
2867153 ATAATT-TATATAATATTTATATTATATTATAATT
1 ATAATTATAT-TAATATTTATATTATA-TATAATT
*
2867187 ATAATTATATTTAAAATATTTTTATT-TATATAAATT
1 ATAATTATA-TT--AATATTTATATTATATAT-AATT
*
2867223 TTAA-TATATTAATAATTTATATTATATATA
1 ATAATTATATTAAT-ATTTATATTATATATA
2867253 TTTTAAAAAT
Statistics
Matches: 56, Mismatches: 3, Indels: 15
0.76 0.04 0.20
Matches are distributed among these distances:
32 3 0.05
33 9 0.16
34 13 0.23
35 10 0.18
36 10 0.18
37 11 0.20
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (33 bp):
ATAATTATATTAATATTTATATTATATATAATT
Found at i:2875002 original size:26 final size:26
Alignment explanation
Indices: 2874945--2875003 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
2874935 AAAAATTATT
* *
2874945 TATATT-TTAAAATTTTTTAATAATA
1 TATATTATTAAAATTTATTAATAAAA
2874970 TATTATTATT-AAATTTATTAATAAAA
1 TA-TATTATTAAAATTTATTAATAAAA
2874996 TGATATTA
1 T-ATATTA
2875004 ATATATCAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
25 2 0.07
26 24 0.83
27 3 0.10
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (26 bp):
TATATTATTAAAATTTATTAATAAAA
Found at i:2881803 original size:2 final size:2
Alignment explanation
Indices: 2881798--2881826 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2881788 ACGCCTGTAC
2881798 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2881827 ACAAATATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2888127 original size:2 final size:2
Alignment explanation
Indices: 2888122--2888146 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2888112 GTTTAATTTG
2888122 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2888147 AAAGTTTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2888217 original size:24 final size:25
Alignment explanation
Indices: 2888182--2888228 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
2888172 AAAATATGAT
*
2888182 ATTTTATTAATAA-ATAA-ATAAAA
1 ATTTTATAAATAATATAATATAAAA
2888205 ATTTTAATAAATAATATAATATAA
1 ATTTT-ATAAATAATATAATATAA
2888229 TTCATTATCG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 5 0.25
24 7 0.35
25 4 0.20
26 4 0.20
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (25 bp):
ATTTTATAAATAATATAATATAAAA
Found at i:2888797 original size:2 final size:2
Alignment explanation
Indices: 2888790--2888825 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2888780 AACCAAATGA
2888790 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2888826 TCTTGCAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2891368 original size:2 final size:2
Alignment explanation
Indices: 2891355--2891389 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
2891345 GAATCTGAGG
*
2891355 TA TA TT TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2891390 TCATTTGAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:2892197 original size:26 final size:25
Alignment explanation
Indices: 2892167--2892226 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 25
2892157 AATTTCTGAA
2892167 TTATTTTATT-TTTAAAGTAATTTTTT
1 TTATTTTATTATTTAAA-T-ATTTTTT
2892193 TTATTTTTATTACATTTAAATATTTTTT
1 TTA-TTTTATT--ATTTAAATATTTTTT
2892221 TTATTT
1 TTATTT
2892227 ATACGGACTT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
26 3 0.10
27 10 0.33
28 10 0.33
29 1 0.03
30 6 0.20
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.70
Consensus pattern (25 bp):
TTATTTTATTATTTAAATATTTTTT
Found at i:2892203 original size:27 final size:26
Alignment explanation
Indices: 2892170--2892226 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 26
2892160 TTCTGAATTA
2892170 TTTTATT-TTTAAAGTAATTTTTTTTAT
1 TTTTATTATTTAAA-T-ATTTTTTTTAT
2892197 TTTTATTACATTTAAATATTTTTTTTAT
1 TTTTATT--ATTTAAATATTTTTTTTAT
2892225 TT
1 TT
2892227 ATACGGACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
27 7 0.26
28 13 0.48
29 1 0.04
30 6 0.22
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (26 bp):
TTTTATTATTTAAATATTTTTTTTAT
Found at i:2898920 original size:17 final size:17
Alignment explanation
Indices: 2898898--2898933 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
2898888 ACTAGTTGTC
2898898 GGTTCTTTTGCGCACGT
1 GGTTCTTTTGCGCACGT
2898915 GGTTCTTTTGCGCACGT
1 GGTTCTTTTGCGCACGT
2898932 GG
1 GG
2898934 CATATCAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.06, C:0.22, G:0.33, T:0.39
Consensus pattern (17 bp):
GGTTCTTTTGCGCACGT
Found at i:2903779 original size:5 final size:6
Alignment explanation
Indices: 2903736--2903777 Score: 70
Period size: 6 Copynumber: 7.3 Consensus size: 6
2903726 ATATATTCAA
2903736 TTTAAT TTTAAT TTTAAT TTTAAT TTTAA- TTTAA- TTTAAT TT
1 TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT TT
2903778 AAAAATTAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
5 10 0.29
6 25 0.71
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TTTAAT
Found at i:2903890 original size:104 final size:102
Alignment explanation
Indices: 2903681--2903875 Score: 266
Period size: 104 Copynumber: 1.9 Consensus size: 102
2903671 AAAATTAAAA
* * * * * *
2903681 AAAATCTTTGCATCAAACTTAAGTTTATTAATTCAATTTGATTATATATATTCAATTTAATTTTA
1 AAAATATTTGAATCAAACTGAAATTTATTAATCCAATTTAATTATATATATTCAATTTAATTTTA
* *
2903746 ATTTTAATTTTAATTTTAATTTAATTTAATTTAAAAATT
66 ATTTTAATTTTAATTTAAAATTAA--TAATTTAAAAATT
2903785 AAAATATTTGAATCAAACTGAAATTTATTAATCCAATTTAATTATATATGATATTCAATTTAATT
1 AAAATATTTGAATCAAACTGAAATTTATTAATCCAATTTAA-T-TATAT-ATATTCAATTTAATT
2903850 TTAATTTTAA-TTTAATTTAAAATTAA
63 TTAATTTTAATTTTAATTTAAAATTAA
2903876 AATATTATGC
Statistics
Matches: 80, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
104 35 0.44
105 1 0.01
106 19 0.24
107 25 0.31
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.49
Consensus pattern (102 bp):
AAAATATTTGAATCAAACTGAAATTTATTAATCCAATTTAATTATATATATTCAATTTAATTTTA
ATTTTAATTTTAATTTAAAATTAATAATTTAAAAATT
Found at i:2906178 original size:21 final size:21
Alignment explanation
Indices: 2906134--2906325 Score: 87
Period size: 21 Copynumber: 8.9 Consensus size: 21
2906124 GAAAGGGAAA
*
2906134 GAGAGAAAGAGGAAGAGAGGAG
1 GAGAGAAAGAGGAAGA-AGCAG
2906156 GAGAG-AAGAGGAAGAAGCCAG
1 GAGAGAAAGAGGAAGAAG-CAG
*
2906177 GA-AGAAAGAGGAGGAAG-AG
1 GAGAGAAAGAGGAAGAAGCAG
*
2906196 GAGGCCAGAAAGA-GAA-AAGAAG
1 GA-G--AGAAAGAGGAAGAAGCAG
* * *
2906218 AAGA-AGAAGAAGAAGAAGCTAA
1 GAGAGA-AAGAGGAAGAAGC-AG
*
2906240 GA-AGAAAGAGGAAG-AGGAG
1 GAGAGAAAGAGGAAGAAGCAG
**
2906259 GCCAGAAAGAGGAAGGAA-CAG
1 GAGAGAAAGAGGAA-GAAGCAG
*
2906280 GAAGAGGAAGAAGAAGAAGAAGCAG
1 G-AGA-G-A-AAGAGGAAGAAGCAG
*
2906305 CTAAGAAGAAAGAGGAAGAAG
1 --GAG-AGAAAGAGGAAGAAG
2906326 AGGCCCAAAA
Statistics
Matches: 130, Mismatches: 17, Indels: 44
0.68 0.09 0.23
Matches are distributed among these distances:
18 1 0.01
19 11 0.08
20 20 0.15
21 45 0.35
22 15 0.12
23 8 0.06
24 15 0.12
25 11 0.08
26 3 0.02
27 1 0.01
ACGTcount: A:0.54, C:0.05, G:0.40, T:0.01
Consensus pattern (21 bp):
GAGAGAAAGAGGAAGAAGCAG
Found at i:2906178 original size:24 final size:22
Alignment explanation
Indices: 2906132--2906328 Score: 83
Period size: 24 Copynumber: 9.0 Consensus size: 22
2906122 TCGAAAGGGA
2906132 AAGAGAGAAAGAGGAAG-AGAGG
1 AAGAGAG-AAGAGGAAGAAGAGG
*
2906154 AGGAGAGAAGAGGAAGAAGCCAGG
1 AAGAGAGAAGAGGAAGAAG--AGG
* * *
2906178 AAGAAAGAGGAGGAAGAGGAGG
1 AAGAGAGAAGAGGAAGAAGAGG
** *
2906200 -CCAGA-AAGA-GAA-AAGAAG
1 AAGAGAGAAGAGGAAGAAGAGG
* **
2906218 AAGA-AGAAGAAGAAGAAG-CT
1 AAGAGAGAAGAGGAAGAAGAGG
*
2906238 AAGA-AGAAAGAGGAAGAGGAGG
1 AAGAGAG-AAGAGGAAGAAGAGG
** *
2906260 -CCAGA-AAGAGGAAGGAACAGG
1 AAGAGAGAAGAGGAA-GAAGAGG
* *
2906281 AAGAGGAAGAAGAAGAAGAAGCAGCT
1 AAGA-G-AGAAGAGGAAGAAG-AG-G
2906307 AAGA-AGAAAGAGGAAGAAGAGG
1 AAGAGAG-AAGAGGAAGAAGAGG
2906329 CCCAAAAGAG
Statistics
Matches: 127, Mismatches: 30, Indels: 36
0.66 0.16 0.19
Matches are distributed among these distances:
18 5 0.04
19 8 0.06
20 20 0.16
21 30 0.24
22 13 0.10
23 5 0.04
24 33 0.26
25 9 0.07
26 4 0.03
ACGTcount: A:0.54, C:0.05, G:0.40, T:0.01
Consensus pattern (22 bp):
AAGAGAGAAGAGGAAGAAGAGG
Found at i:2906218 original size:3 final size:3
Alignment explanation
Indices: 2906208--2906326 Score: 60
Period size: 3 Copynumber: 37.0 Consensus size: 3
2906198 GGCCAGAAAG
*
2906208 AGA A-A AGA AGA AGA AGA AGA AGA AGA AGCTA AGA AGAA AGA GGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AG--A AGA AG-A AGA AGA AGA
* * * * * * * *
2906255 GGA GGCC AGAA AGA GGA AGGA ACA GGA AGA GGA AGA AGA AGA AGA AGC
1 AGA AG-A AG-A AGA AGA A-GA AGA AGA AGA AGA AGA AGA AGA AGA AGA
*
2906303 AGCTA AGA AGAA AGA GGA AGA AGA
1 AG--A AGA AG-A AGA AGA AGA AGA
2906327 GGCCCAAAAG
Statistics
Matches: 88, Mismatches: 19, Indels: 18
0.70 0.15 0.14
Matches are distributed among these distances:
2 2 0.02
3 69 0.78
4 12 0.14
5 5 0.06
ACGTcount: A:0.57, C:0.05, G:0.36, T:0.02
Consensus pattern (3 bp):
AGA
Found at i:2906286 original size:16 final size:15
Alignment explanation
Indices: 2906248--2906289 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
2906238 AAGAAGAAAG
*
2906248 AGGAAGAGG-AGGCC
1 AGGAAGAGGAAGGAC
*
2906262 AGAAAGAGGAAGGAAC
1 AGGAAGAGGAAGG-AC
2906278 AGGAAGAGGAAG
1 AGGAAGAGGAAG
2906290 AAGAAGAAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
14 8 0.35
15 3 0.13
16 12 0.52
ACGTcount: A:0.48, C:0.07, G:0.45, T:0.00
Consensus pattern (15 bp):
AGGAAGAGGAAGGAC
Found at i:2906324 original size:10 final size:9
Alignment explanation
Indices: 2906140--2906440 Score: 74
Period size: 9 Copynumber: 30.4 Consensus size: 9
2906130 GAAAGAGAGA
2906140 AAGAGGAAG
1 AAGAGGAAG
2906149 AGAGGAGGAGAG
1 A-A-GAGGA-AG
2906161 AAGAGGAAG
1 AAGAGGAAG
2906170 AAGCCAGGAAG
1 AAG--AGGAAG
*
2906181 AAAGAGGAGG
1 -AAGAGGAAG
2906191 AAGAGGAGGCCAG
1 AAGAGGA----AG
*
2906204 AAAGAGAAAAG
1 -AAGAG-GAAG
*
2906215 AAGAAGAAG
1 AAGAGGAAG
*
2906224 AAGAAGAAG
1 AAGAGGAAG
*
2906233 AAGCTAAGAAG
1 AAG--AGGAAG
2906244 AAAGAGGAAG
1 -AAGAGGAAG
* *
2906254 AGGAGGCCAG
1 AAGAGG-AAG
2906264 AAAGAGGAAGG
1 -AAGAGGAA-G
*
2906275 AACAGGAAG
1 AAGAGGAAG
* *
2906284 AGGAAGAAG
1 AAGAGGAAG
*
2906293 AAGAAGAAG
1 AAGAGGAAG
* *
2906302 CAGCTAAGAAG
1 AAG--AGGAAG
2906313 AAAGAGGAAG
1 -AAGAGGAAG
2906323 AAGAGGCCCAA-
1 AAGAGG---AAG
2906334 AAGAGGAAGG
1 AAGAGGAA-G
*
2906344 AACA-G--G
1 AAGAGGAAG
2906350 AAGAGGAAG
1 AAGAGGAAG
**
2906359 AAGAGGCCCG
1 AAGAGG-AAG
*
2906369 AAAGAGAAAAG
1 -AAGAG-GAAG
2906380 AAGAGGAAG
1 AAGAGGAAG
*
2906389 ACGAAGCGAAG
1 AAG-AG-GAAG
*
2906400 AAGAGGGAGG
1 AAGA-GGAAG
* *
2906410 AGGAGGAGG
1 AAGAGGAAG
2906419 AA-AGGAAG
1 AAGAGGAAG
2906427 -AGAAGAGAAG
1 AAG-AG-GAAG
2906437 AAGA
1 AAGA
2906441 AGCAAGGAAA
Statistics
Matches: 221, Mismatches: 32, Indels: 77
0.67 0.10 0.23
Matches are distributed among these distances:
6 4 0.02
7 2 0.01
8 7 0.03
9 77 0.35
10 58 0.26
11 53 0.24
12 13 0.06
13 1 0.00
14 5 0.02
15 1 0.00
ACGTcount: A:0.52, C:0.06, G:0.41, T:0.01
Consensus pattern (9 bp):
AAGAGGAAG
Found at i:2906345 original size:63 final size:63
Alignment explanation
Indices: 2906139--2906362 Score: 208
Period size: 69 Copynumber: 3.5 Consensus size: 63
2906129 GGAAAGAGAG
* * * * *
2906139 AAAGAGGAAGAGAGGAGGAGAGAAGAGGAAGAAGC--C-AGGAAGAAAGAGGAGGAAGAGGAGGC
1 AAAGAGGAAG-GAAGAGGA-AGAAGAAGAAGAAGCAGCTAAGAAGAAAGAGGAAGAAGA-G-GCC
2906201 CA
62 CA
* * * *
2906203 GAAAGA-GAA--AAGAAGAAGAAGAAGAAGAAGAAGCTAAGAAGAAAGAGGAAGAGGAGGCCAGA
1 -AAAGAGGAAGGAAGAGGAAGAAGAAGAAGAAGCAGCTAAGAAGAAAGAGGAAGAAGAGGCC-CA
2906265 AAGAGGAAGGAACAGGAAGAGGAAGAAGAAGAAGAAGCAGCTAAGAAGAAAGAGGAAGAAGAGGC
1 AA-A-G-AGG-A-AGGAAGAGGAAGAAGAAGAAGAAGCAGCTAAGAAGAAAGAGGAAGAAGAGGC
2906330 CCA
61 CCA
* *
2906333 AAAGAGGAAGGAACAGGAAGAGGAAGAAGA
1 AAAGAGGAAGGAAGAGGAAGAAGAAGAAGA
2906363 GGCCCGAAAG
Statistics
Matches: 132, Mismatches: 15, Indels: 26
0.76 0.09 0.15
Matches are distributed among these distances:
60 13 0.10
61 9 0.07
62 4 0.03
63 38 0.29
64 5 0.04
65 9 0.07
66 2 0.02
67 2 0.02
68 3 0.02
69 47 0.36
ACGTcount: A:0.54, C:0.06, G:0.39, T:0.01
Consensus pattern (63 bp):
AAAGAGGAAGGAAGAGGAAGAAGAAGAAGAAGCAGCTAAGAAGAAAGAGGAAGAAGAGGCCCA
Found at i:2906354 original size:36 final size:35
Alignment explanation
Indices: 2906245--2906394 Score: 130
Period size: 36 Copynumber: 4.3 Consensus size: 35
2906235 GCTAAGAAGA
*
2906245 AAGAGGAAGAGGAGGCCAGAAAGAGGAAGGAACAGG
1 AAGAGGAAGAAGAGGCCA-AAAGAGGAAGGAACAGG
* * *
2906281 AAGAGGAAGAAGAAG--AAGAAGCAGCTAA-G-A-AGA
1 AAGAGGAAGAAGAGGCCAA-AAG-AG-GAAGGAACAGG
2906314 AAGAGGAAGAAGAGGCCCAAAAGAGGAAGGAACAGG
1 AAGAGGAAGAAGAGG-CCAAAAGAGGAAGGAACAGG
* * * *
2906350 AAGAGGAAGAAGAGGCCCGAAAGAGAAAAGAAGAGG
1 AAGAGGAAGAAGAGG-CCAAAAGAGGAAGGAACAGG
*
2906386 AAGACGAAG
1 AAGAGGAAG
2906395 CGAAGAAGAG
Statistics
Matches: 93, Mismatches: 12, Indels: 18
0.76 0.10 0.15
Matches are distributed among these distances:
33 19 0.20
34 8 0.09
35 7 0.08
36 59 0.63
ACGTcount: A:0.52, C:0.09, G:0.39, T:0.01
Consensus pattern (35 bp):
AAGAGGAAGAAGAGGCCAAAAGAGGAAGGAACAGG
Found at i:2906388 original size:6 final size:6
Alignment explanation
Indices: 2906379--2906463 Score: 50
Period size: 6 Copynumber: 13.7 Consensus size: 6
2906369 AAAGAGAAAA
* * * *
2906379 GAAGAG GAAGAC GAAGCGAA GAAGAGG GAGGAG GAGGAG GAA-AG GAAGA-
1 GAAGAG GAAGAG GAA--GAG GAAGA-G GAAGAG GAAGAG GAAGAG GAAGAG
*
2906428 GAAGA- GAAGAA GAAGCAAG GAAAGAG GAAGAG GAAG
1 GAAGAG GAAGAG GAAG--AG G-AAGAG GAAGAG GAAG
2906464 CCCGAAGACA
Statistics
Matches: 65, Mismatches: 6, Indels: 16
0.75 0.07 0.18
Matches are distributed among these distances:
5 15 0.23
6 33 0.51
7 7 0.11
8 7 0.11
9 3 0.05
ACGTcount: A:0.51, C:0.04, G:0.46, T:0.00
Consensus pattern (6 bp):
GAAGAG
Found at i:2906551 original size:3 final size:3
Alignment explanation
Indices: 2906503--2906534 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
2906493 AGAGCGAGGC
*
2906503 AAG AAG AAG AAG AAG AAG AAG AGG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
2906535 AGGAAACGAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:2909772 original size:166 final size:163
Alignment explanation
Indices: 2909499--2909831 Score: 558
Period size: 166 Copynumber: 2.0 Consensus size: 163
2909489 AATGCCTGAG
* * * *
2909499 ACTAGCCAGTGTCAGAAAAGTTTAAGTATATTTTAAGCCATTACTTAAATATAATTTGTAAAATG
1 ACTAGCCAGTGTCAAAAAAGTTTAAGTATATTTTAAGCCATAACTTAAAGATAATTTGCAAAATG
* * *
2909564 GAAAAAGGTAAAAAAGGGACAAAAAGTAACATATAAAAATAAAAAGAAGATGAGAGGGGACATAC
66 GAAAAAGGTAAAAAAAGGACAAAAAATAACATATAAAAATAAAAAGAAGACGAGA--GGACATAC
*
2909629 TGTTCAATTAAACTTGTGGTCTGTTCATCCTTAGA
129 TGTTCAATTAAACTTGCGGTCTGTTCATCCTTAGA
*
2909664 ACTAGCCAGTGTCAAAAAAGTTTTAAGTATATTTTAGGCCATAACTTAAAGATAATTTGCAAAAT
1 ACTAGCCAGTGTCAAAAAAG-TTTAAGTATATTTTAAGCCATAACTTAAAGATAATTTGCAAAAT
2909729 GGAAAAAGGTAAAAAAAGGACAAAAAATAACATATAAAAATAAAAAGAAGACGAGAGGACATACT
65 GGAAAAAGGTAAAAAAAGGACAAAAAATAACATATAAAAATAAAAAGAAGACGAGAGGACATACT
2909794 GTTCAATTAAACTTGCGGTCTGTTCATCCTTAGA
130 GTTCAATTAAACTTGCGGTCTGTTCATCCTTAGA
2909828 ACTA
1 ACTA
2909832 CCATCAAACG
Statistics
Matches: 158, Mismatches: 9, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
164 46 0.29
165 19 0.12
166 93 0.59
ACGTcount: A:0.45, C:0.11, G:0.17, T:0.26
Consensus pattern (163 bp):
ACTAGCCAGTGTCAAAAAAGTTTAAGTATATTTTAAGCCATAACTTAAAGATAATTTGCAAAATG
GAAAAAGGTAAAAAAAGGACAAAAAATAACATATAAAAATAAAAAGAAGACGAGAGGACATACTG
TTCAATTAAACTTGCGGTCTGTTCATCCTTAGA
Found at i:2911697 original size:20 final size:20
Alignment explanation
Indices: 2911667--2911720 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
2911657 AATTTATTTT
*
2911667 TATTTTTAAATTCATGTAAAA
1 TATTTTAAAATTCAT-TAAAA
*
2911688 -ATTTTAAAATATTATTAAAA
1 TATTTTAAAAT-TCATTAAAA
2911708 TATTTATAAAATT
1 TATTT-TAAAATT
2911721 AAAAAATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
20 14 0.50
21 8 0.29
22 6 0.21
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (20 bp):
TATTTTAAAATTCATTAAAA
Found at i:2911760 original size:21 final size:20
Alignment explanation
Indices: 2911723--2911775 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 20
2911713 ATAAAATTAA
2911723 AAAATAAA-TTAAATCAATT
1 AAAATAAATTTAAATCAATT
*
2911742 TAAATAAATTTAAATTCAATT
1 AAAATAAATTTAAA-TCAATT
*
2911763 AAAATTAATTTAA
1 AAAATAAATTTAA
2911776 TCCTACATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 7 0.24
20 5 0.17
21 17 0.59
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (20 bp):
AAAATAAATTTAAATCAATT
Found at i:2911775 original size:11 final size:10
Alignment explanation
Indices: 2911731--2911775 Score: 54
Period size: 10 Copynumber: 4.4 Consensus size: 10
2911721 AAAAAATAAA
*
2911731 TTAAATCAAT
1 TTAAATTAAT
*
2911741 TTAAATAAAT
1 TTAAATTAAT
2911751 TTAAATTCAAT
1 TTAAATT-AAT
*
2911762 TAAAATTAAT
1 TTAAATTAAT
2911772 TTAA
1 TTAA
2911776 TCCTACATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
10 21 0.70
11 9 0.30
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.42
Consensus pattern (10 bp):
TTAAATTAAT
Found at i:2912273 original size:33 final size:36
Alignment explanation
Indices: 2912207--2912276 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 36
2912197 CAATATTACC
2912207 ATGTAATATGAATATAAATAAAAAAAATATAATATA
1 ATGTAATATGAATATAAATAAAAAAAATATAATATA
2912243 ATGTAAATAT-AATA-AAAT-AAAAAAAT-TAATATA
1 ATGT-AATATGAATATAAATAAAAAAAATATAATATA
2912276 A
1 A
2912277 ATATATTAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
33 8 0.24
34 8 0.24
35 4 0.12
36 8 0.24
37 5 0.15
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (36 bp):
ATGTAATATGAATATAAATAAAAAAAATATAATATA
Found at i:2912296 original size:15 final size:14
Alignment explanation
Indices: 2912231--2912300 Score: 59
Period size: 14 Copynumber: 4.8 Consensus size: 14
2912221 TAAATAAAAA
*
2912231 AAATATAATATAATGT
1 AAATAT-AT-TAATAT
* *
2912247 AAATATAATAAAAT
1 AAATATATTAATAT
* *
2912261 AAAAAAATTAATAT
1 AAATATATTAATAT
2912275 AAATATATTAATTAT
1 AAATATATTAA-TAT
*
2912290 TAATATATTAA
1 AAATATATTAA
2912301 ATTTTATATA
Statistics
Matches: 43, Mismatches: 10, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
14 23 0.53
15 14 0.33
16 6 0.14
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.37
Consensus pattern (14 bp):
AAATATATTAATAT
Found at i:2924579 original size:21 final size:17
Alignment explanation
Indices: 2924539--2924573 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
2924529 CCTAGCTTCC
2924539 TAAGTTATCAATATGTA
1 TAAGTTATCAATATGTA
2924556 TAAGTTATCAATATGTA
1 TAAGTTATCAATATGTA
2924573 T
1 T
2924574 GAATAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.40, C:0.06, G:0.11, T:0.43
Consensus pattern (17 bp):
TAAGTTATCAATATGTA
Found at i:2925181 original size:17 final size:16
Alignment explanation
Indices: 2925149--2925183 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
2925139 AGTATTCGTC
*
2925149 ATATTTTTATTTAAAT
1 ATATTTTTATTAAAAT
2925165 ATATTTTTATATAAAAT
1 ATATTTTTAT-TAAAAT
2925182 AT
1 AT
2925184 GGTTGAAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
ATATTTTTATTAAAAT
Found at i:2926044 original size:13 final size:14
Alignment explanation
Indices: 2926028--2926060 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
2926018 ATATTTTAAT
*
2926028 TTAATAAAATTTA-
1 TTAATAAAAATTAG
2926041 TTAATAAAAATTAG
1 TTAATAAAAATTAG
2926055 TTAATA
1 TTAATA
2926061 TTAATATAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (14 bp):
TTAATAAAAATTAG
Found at i:2926307 original size:15 final size:15
Alignment explanation
Indices: 2926287--2926337 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
2926277 CAGTACAATC
2926287 ATATTTAATTATTTT
1 ATATTTAATTATTTT
*
2926302 ATATTT-ATATATTTA
1 ATATTTAAT-TATTTT
*
2926317 ATATGTTAATAATTTTT
1 ATAT-TTAATTA-TTTT
2926334 ATAT
1 ATAT
2926338 ATAAATTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
14 2 0.07
15 15 0.52
16 3 0.10
17 9 0.31
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (15 bp):
ATATTTAATTATTTT
Found at i:2926312 original size:8 final size:8
Alignment explanation
Indices: 2926287--2926372 Score: 56
Period size: 8 Copynumber: 10.8 Consensus size: 8
2926277 CAGTACAATC
2926287 ATATTTA-
1 ATATTTAT
2926294 ATTATTT-T
1 A-TATTTAT
2926302 ATATTTAT
1 ATATTTAT
2926310 ATATTTA-
1 ATATTTAT
2926317 ATATGTTA-
1 ATAT-TTAT
*
2926325 ATAATTTTT
1 AT-ATTTAT
* *
2926334 ATATATAA
1 ATATTTAT
*
2926342 AT-TTTAA
1 ATATTTAT
2926349 ATTATTTAT
1 A-TATTTAT
2926358 ATATTTAT
1 ATATTTAT
2926366 ATTATTT
1 A-TATTT
2926373 TTTAAATCAA
Statistics
Matches: 64, Mismatches: 6, Indels: 16
0.74 0.07 0.19
Matches are distributed among these distances:
7 15 0.23
8 35 0.55
9 14 0.22
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.60
Consensus pattern (8 bp):
ATATTTAT
Found at i:2926336 original size:24 final size:22
Alignment explanation
Indices: 2926287--2926368 Score: 69
Period size: 24 Copynumber: 3.5 Consensus size: 22
2926277 CAGTACAATC
*
2926287 ATATTTAATTATTTTATATTTAT
1 ATATTTAA-TATTTAATATTTAT
*
2926310 ATATTTAATATGTTAATAATTTTT
1 ATATTTAATAT-TTAAT-ATTTAT
*
2926334 ATATATAA-ATTTTAAATTATTTAT
1 ATATTTAATA-TTT-AA-TATTTAT
2926358 ATATTT-ATATT
1 ATATTTAATATT
2926369 ATTTTTTAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
22 3 0.06
23 18 0.38
24 26 0.54
25 1 0.02
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (22 bp):
ATATTTAATATTTAATATTTAT
Found at i:2926404 original size:20 final size:19
Alignment explanation
Indices: 2926337--2926413 Score: 74
Period size: 17 Copynumber: 4.2 Consensus size: 19
2926327 AATTTTTATA
2926337 TATAAATTTTAAATTA--TT
1 TATAAA-TTTAAATTATTTT
* *
2926355 TATATATTTATATTATTTT
1 TATAAATTTAAATTATTTT
*
2926374 T-TAAA-TCAAATTATTTT
1 TATAAATTTAAATTATTTT
2926391 TATCAAATTTAAATT-TTTT
1 TAT-AAATTTAAATTATTTT
2926410 TATA
1 TATA
2926414 TTATATTTAA
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
17 19 0.40
18 10 0.21
19 13 0.27
20 6 0.12
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (19 bp):
TATAAATTTAAATTATTTT
Found at i:2927085 original size:6 final size:6
Alignment explanation
Indices: 2927074--2927125 Score: 58
Period size: 6 Copynumber: 9.2 Consensus size: 6
2927064 AAATTAAATC
*
2927074 AAATTA AAATTA AGAA--A ATATTA AAATTA AAATT- AAATT- AAATTA
1 AAATTA AAATTA A-AATTA AAATTA AAATTA AAATTA AAATTA AAATTA
2927119 AAATTA A
1 AAATTA A
2927126 TTTAAATATT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
4 1 0.03
5 12 0.30
6 25 0.62
7 2 0.05
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (6 bp):
AAATTA
Found at i:2927121 original size:16 final size:16
Alignment explanation
Indices: 2927063--2927132 Score: 65
Period size: 16 Copynumber: 4.3 Consensus size: 16
2927053 ATAGTATTTA
*
2927063 TAAATT-AAATCAAAT
1 TAAATTAAAATTAAAT
2927078 TAAAATTAAGAA--AATAT
1 T-AAATTAA-AATTAA-AT
2927095 TAAAATTAAAATTAAAT
1 T-AAATTAAAATTAAAT
*
2927112 TAAATTAAAATTAATT
1 TAAATTAAAATTAAAT
2927128 TAAAT
1 TAAAT
2927133 ATTTATATTA
Statistics
Matches: 48, Mismatches: 1, Indels: 11
0.80 0.02 0.18
Matches are distributed among these distances:
15 1 0.02
16 28 0.58
17 15 0.31
18 4 0.08
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.36
Consensus pattern (16 bp):
TAAATTAAAATTAAAT
Found at i:2928684 original size:29 final size:30
Alignment explanation
Indices: 2928642--2928717 Score: 109
Period size: 30 Copynumber: 2.6 Consensus size: 30
2928632 TTTAAAGAAG
2928642 TTTTTAATATTTAATTTGGATC-AAATAAA
1 TTTTTAATATTTAATTTGGATCTAAATAAA
* * *
2928671 TTTTTTATTTTTAATTTGTATCTAAATAAA
1 TTTTTAATATTTAATTTGGATCTAAATAAA
*
2928701 TTTTTAATAATTAATTT
1 TTTTTAATATTTAATTT
2928718 ATACTTAAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
29 19 0.47
30 21 0.52
ACGTcount: A:0.37, C:0.03, G:0.04, T:0.57
Consensus pattern (30 bp):
TTTTTAATATTTAATTTGGATCTAAATAAA
Found at i:2928727 original size:30 final size:29
Alignment explanation
Indices: 2928633--2928729 Score: 104
Period size: 30 Copynumber: 3.3 Consensus size: 29
2928623 TTTATTACAT
* * *
2928633 TTAAAGAAGTTTTTAATATTTAATTTGGA
1 TTAAATAAATTTTTAATATTTAATTTGTA
* * *
2928662 TCAAATAAATTTTTTATTTTTAATTTGTA
1 TTAAATAAATTTTTAATATTTAATTTGTA
* *
2928691 TCTAAATAAATTTTTAATAATTAATTTATA
1 T-TAAATAAATTTTTAATATTTAATTTGTA
2928721 CTTAAATAA
1 -TTAAATAA
2928730 TCTTTAAGAT
Statistics
Matches: 55, Mismatches: 11, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
29 24 0.44
30 30 0.55
31 1 0.02
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (29 bp):
TTAAATAAATTTTTAATATTTAATTTGTA
Found at i:2929238 original size:13 final size:13
Alignment explanation
Indices: 2929215--2929266 Score: 56
Period size: 12 Copynumber: 4.0 Consensus size: 13
2929205 TTTTAAAAAA
2929215 TTTAT-ATTAATT
1 TTTATAATTAATT
2929227 TTTATAATTAA-T
1 TTTATAATTAATT
2929239 TTTA-AATATAATAT
1 TTTATAAT-TAAT-T
2929253 TTTATTAATTAATT
1 TTTA-TAATTAATT
2929267 GTAGTTAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
11 3 0.09
12 13 0.38
13 5 0.15
14 6 0.18
15 4 0.12
16 3 0.09
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TTTATAATTAATT
Found at i:2929574 original size:75 final size:76
Alignment explanation
Indices: 2929483--2929629 Score: 172
Period size: 76 Copynumber: 1.9 Consensus size: 76
2929473 CTATATTCCT
* ** * * **
2929483 TCGGCGGTTGCAAACTCACGGCAC-CAAACTCCAAACCCTCA-CAAGTGACCTGAGCAACTCCGA
1 TCGGCGGTTGAAAACTCACAACACTAAAACCCCAAACCCTCAGC-AGTGACAGGAGCAACTCCGA
2929546 TAAGAAACTCCG
65 TAAGAAACTCCG
* * *
2929558 TCGGCGGTTTAAAACTCACAACACTAAAACCCCAAACCTTTAGCAGTGACAGGAGCAACTCCGAT
1 TCGGCGGTTGAAAACTCACAACACTAAAACCCCAAACCCTCAGCAGTGACAGGAGCAACTCCGAT
*
2929623 AGGAAAC
66 AAGAAAC
2929630 ATCTAAAATG
Statistics
Matches: 59, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
75 20 0.34
76 38 0.64
77 1 0.02
ACGTcount: A:0.35, C:0.31, G:0.18, T:0.16
Consensus pattern (76 bp):
TCGGCGGTTGAAAACTCACAACACTAAAACCCCAAACCCTCAGCAGTGACAGGAGCAACTCCGAT
AAGAAACTCCG
Found at i:2931625 original size:2 final size:2
Alignment explanation
Indices: 2931618--2931652 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2931608 TTAATTAGAT
2931618 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2931653 TTCTTTTTCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Done.