Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002755.1 Hibiscus syriacus cultivar Beakdansim tig00005678_pilon, whole genome shotgun sequence
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: 722678
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
File 4 of 4
Found at i:561351 original size:53 final size:53
Alignment explanation
Indices: 561288--561450 Score: 263
Period size: 53 Copynumber: 3.1 Consensus size: 53
561278 CTAAGGTATT
* * *
561288 AAAATGGTAATTCACAAACTCATTATGAATATCATGGGTGCATACATAGTGTC
1 AAAATGGTAATTCACAAACTCATTATGAATACCATGGATGCACACATAGTGTC
*
561341 AAAATGGTAATTCATAAACTCATTATGAATACCATGGATGCACACATAGTGTC
1 AAAATGGTAATTCACAAACTCATTATGAATACCATGGATGCACACATAGTGTC
* * *
561394 GAAATGGTAATTTACAAACTCATTATGAATACCATGGATGCACACAGAGTGTC
1 AAAATGGTAATTCACAAACTCATTATGAATACCATGGATGCACACATAGTGTC
561447 AAAA
1 AAAA
561451 GTACACATAG
Statistics
Matches: 101, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
53 101 1.00
ACGTcount: A:0.40, C:0.16, G:0.17, T:0.28
Consensus pattern (53 bp):
AAAATGGTAATTCACAAACTCATTATGAATACCATGGATGCACACATAGTGTC
Found at i:561532 original size:48 final size:48
Alignment explanation
Indices: 561466--561566 Score: 150
Period size: 48 Copynumber: 2.1 Consensus size: 48
561456 CATAGCACTG
561466 ATACAAAATTGTAACATATGCATTAAACAAAATCGATCGATAACCATC
1 ATACAAAATTGTAACATATGCATTAAACAAAATCGATCGATAACCATC
* * * *
561514 ATACGAAAA-TGTAGCATATGTATTAAACAAAATCGATTGATATCCATC
1 ATAC-AAAATTGTAACATATGCATTAAACAAAATCGATCGATAACCATC
561562 ATACA
1 ATACA
561567 TAAAGTATGT
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
47 1 0.02
48 43 0.90
49 4 0.08
ACGTcount: A:0.47, C:0.17, G:0.10, T:0.27
Consensus pattern (48 bp):
ATACAAAATTGTAACATATGCATTAAACAAAATCGATCGATAACCATC
Found at i:561603 original size:18 final size:18
Alignment explanation
Indices: 561580--561622 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
561570 AGTATGTCGA
561580 AATGCACCTATGACTCTC
1 AATGCACCTATGACTCTC
561598 AATGCACCTATGACTCTC
1 AATGCACCTATGACTCTC
*
561616 CATGCAC
1 AATGCAC
561623 ATGCAATAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.28, C:0.35, G:0.12, T:0.26
Consensus pattern (18 bp):
AATGCACCTATGACTCTC
Found at i:562219 original size:20 final size:20
Alignment explanation
Indices: 562174--562225 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
562164 TCTTTACTTA
*
562174 CAGTATCGATACCTTACCAT
1 CAGTATCGATACATTACCAT
**
562194 TGGTATCGATACATT-CACAT
1 CAGTATCGATACATTAC-CAT
562214 CAGTATCGATAC
1 CAGTATCGATAC
562226 TTCTTCAACC
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 1 0.04
20 25 0.96
ACGTcount: A:0.31, C:0.25, G:0.13, T:0.31
Consensus pattern (20 bp):
CAGTATCGATACATTACCAT
Found at i:562850 original size:64 final size:66
Alignment explanation
Indices: 562694--562853 Score: 204
Period size: 65 Copynumber: 2.5 Consensus size: 66
562684 AATTAAATTG
*
562694 AACATCGAATGCATTTCATGCATCGATGCA-CATACAATGCACCGATGCACTTAGGATTTTATGA
1 AACATCGAATGCATTTGATGCATCGATGCACCATACAATGCACCGATGCACTTAGGATTTTATGA
562758 A
66 A
* * * * *
562759 AACATCGAATGCATTTGATGCATCGATGCACCA-GCCATGTATCGATGCACTCT-GGCTATTT-T
1 AACATCGAATGCATTTGATGCATCGATGCACCATACAATGCACCGATGCACT-TAGGAT-TTTAT
562821 G-A
64 GAA
*
562823 AACATCGAATGCACTTGATGCATCGATGCAC
1 AACATCGAATGCATTTGATGCATCGATGCAC
562854 TCTTAGTGCA
Statistics
Matches: 85, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
64 31 0.36
65 48 0.56
66 6 0.07
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.28
Consensus pattern (66 bp):
AACATCGAATGCATTTGATGCATCGATGCACCATACAATGCACCGATGCACTTAGGATTTTATGA
A
Found at i:562853 original size:17 final size:19
Alignment explanation
Indices: 562825--562873 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
562815 TATTTTGAAA
562825 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
562843 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
562862 CATCGATGCACT
1 CATCGATGCACT
562874 AAGGATCCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 7 0.25
18 7 0.25
19 14 0.50
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.29
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:568221 original size:2 final size:2
Alignment explanation
Indices: 568214--568267 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
568204 TCGAACTTAA
568214 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
568256 AT AT AT AT AT AT
1 AT AT AT AT AT AT
568268 GATTTCGAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:570540 original size:65 final size:63
Alignment explanation
Indices: 570421--570630 Score: 221
Period size: 65 Copynumber: 3.3 Consensus size: 63
570411 TTTTTCTGAG
* * *
570421 TGATGCACCGATGCACCAATCCATGCATCGATGCAC-CATGA-ATTAAATTG-AACATCGAATGC
1 TGATGCATCGATGCA-CAA-CCATGCACCGATGCACTCAGGATATT---TTGAAACATCGAATGC
570483 ATT
61 ATT
* *
570486 TCATGCATCGATGCACATACCATGCACCGATGCACTGAGGAT-TTTATGAAAACATCGAATGCAT
1 TGATGCATCGATGCACA-ACCATGCACCGATGCACTCAGGATATTT-TG-AAACATCGAATGCAT
570550 T
63 T
* * * * *
570551 TGATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACT
1 TGATGCATCGATGCA-CAACCATGCACCGATGCACTCAGGATATTTTGAAACATCGAATGCATT
570615 TGATGCATCGATGCAC
1 TGATGCATCGATGCAC
570631 TCTTAGTTCA
Statistics
Matches: 125, Mismatches: 12, Indels: 18
0.81 0.08 0.12
Matches are distributed among these distances:
62 1 0.01
63 3 0.02
64 47 0.38
65 69 0.55
66 5 0.04
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (63 bp):
TGATGCATCGATGCACAACCATGCACCGATGCACTCAGGATATTTTGAAACATCGAATGCATT
Found at i:576875 original size:53 final size:53
Alignment explanation
Indices: 576712--576868 Score: 260
Period size: 53 Copynumber: 3.0 Consensus size: 53
576702 ACTAAGGTAA
* *
576712 CGAAATGGTAATTCACAAACTCATTATGAATATCATGGGTGCACACATAGTGC
1 CGAAATGGTAATTCACAAACTCATTATGAATAACATGGATGCACACATAGTGC
* *
576765 CGAAATGGTAATTCACAAACTCATTATGAATACCATGGATGCACACGTAGTGC
1 CGAAATGGTAATTCACAAACTCATTATGAATAACATGGATGCACACATAGTGC
* *
576818 CGAAATGGTAATTCACAAACTCATTATGAATAAAATGGATGCACGCATAGT
1 CGAAATGGTAATTCACAAACTCATTATGAATAACATGGATGCACACATAGT
576869 TTCGAAAGTA
Statistics
Matches: 97, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
53 97 1.00
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.25
Consensus pattern (53 bp):
CGAAATGGTAATTCACAAACTCATTATGAATAACATGGATGCACACATAGTGC
Found at i:590738 original size:30 final size:27
Alignment explanation
Indices: 590681--590749 Score: 68
Period size: 28 Copynumber: 2.4 Consensus size: 27
590671 CTCAAAACAT
*
590681 TATTATTTTATATATTTAAAATTAATA
1 TATTATTTTATATATTTAAAATAAATA
* *
590708 TATTATTTTAGTATCATTT-TAATAAAAA
1 TATTATTTTA-TAT-ATTTAAAATAAATA
590736 TATTAATTATTATA
1 TATT-ATT-TTATA
590750 ATAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
27 10 0.29
28 13 0.37
29 9 0.26
30 3 0.09
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (27 bp):
TATTATTTTATATATTTAAAATAAATA
Found at i:590755 original size:18 final size:19
Alignment explanation
Indices: 590729--590822 Score: 82
Period size: 21 Copynumber: 4.7 Consensus size: 19
590719 TATCATTTTA
*
590729 ATAAAAATATTA-ATTATT
1 ATAATAATATTATATTATT
*
590747 ATAATAATATTATATTTTT
1 ATAATAATATTATATTATT
** *
590766 ATTGTTATAATTATATTATT
1 ATAATAAT-ATTATATTATT
590786 ATATATATATATTATATTTTATT
1 ATA-ATA-ATATTATA--TTATT
*
590809 TTAATAATATTATA
1 ATAATAATATTATA
590823 CCCTTACGGG
Statistics
Matches: 60, Mismatches: 10, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
18 11 0.18
19 10 0.17
20 12 0.20
21 15 0.25
22 5 0.08
23 7 0.12
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (19 bp):
ATAATAATATTATATTATT
Found at i:590773 original size:14 final size:14
Alignment explanation
Indices: 590754--590808 Score: 60
Period size: 14 Copynumber: 4.1 Consensus size: 14
590744 ATTATAATAA
*
590754 TATTATATTTTTAT
1 TATTATATTTATAT
* *
590768 TGTTATAATTATAT
1 TATTATATTTATAT
*
590782 TATTATATATATA-
1 TATTATATTTATAT
590795 TATTATATTT-TAT
1 TATTATATTTATAT
590808 T
1 T
590809 TTAATAATAT
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
12 2 0.06
13 10 0.30
14 21 0.64
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.64
Consensus pattern (14 bp):
TATTATATTTATAT
Found at i:590778 original size:34 final size:38
Alignment explanation
Indices: 590739--590822 Score: 90
Period size: 40 Copynumber: 2.3 Consensus size: 38
590729 ATAAAAATAT
590739 TAATTATTATAATA-ATAT-TA-TAT-TTTTATTGTT-A
1 TAATTATTATAATATATATATATTATATTTTATT-TTAA
*
590773 TAATTATATTATTATATATATATATTATATTTTATTTTAA
1 TAA-T-TATTATAATATATATATATTATATTTTATTTTAA
590813 TAA-TATTATA
1 TAATTATTATA
590823 CCCTTACGGG
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
34 3 0.07
35 1 0.02
36 9 0.22
37 10 0.24
38 2 0.05
39 5 0.12
40 11 0.27
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.58
Consensus pattern (38 bp):
TAATTATTATAATATATATATATTATATTTTATTTTAA
Found at i:592345 original size:15 final size:16
Alignment explanation
Indices: 592316--592350 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
592306 TAAAAACCGT
*
592316 AAAACCAAACTAAACC
1 AAAACCAAACCAAACC
592332 AAAA-CAAACCAAACC
1 AAAACCAAACCAAACC
592347 AAAA
1 AAAA
592351 ATTTCAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.69, C:0.29, G:0.00, T:0.03
Consensus pattern (16 bp):
AAAACCAAACCAAACC
Found at i:598103 original size:3 final size:3
Alignment explanation
Indices: 598095--598135 Score: 54
Period size: 3 Copynumber: 15.0 Consensus size: 3
598085 AATTCATTTT
598095 TAA TAA TAA -AA TAA TAA TAA -AA -AA T-A TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
598136 ATAAAGACTC
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 8 0.23
3 27 0.77
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:598125 original size:18 final size:18
Alignment explanation
Indices: 598099--598140 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
598089 CATTTTTAAT
598099 AATAAAATAATAATAAAA
1 AATAAAATAATAATAAAA
* *
598117 AATATAATAATAATAATA
1 AATAAAATAATAATAAAA
598135 AATAAA
1 AATAAA
598141 GACTCGGATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (18 bp):
AATAAAATAATAATAAAA
Found at i:598531 original size:43 final size:43
Alignment explanation
Indices: 598477--598627 Score: 147
Period size: 43 Copynumber: 3.6 Consensus size: 43
598467 ATAACACGGT
598477 TCCTACGTGATGAGGACGA-CTGGTTATCTAGGGGTGACACGAC
1 TCCTACGTGATGAGGA-GATCTGGTTATCTAGGGGTGACACGAC
**
598520 TCCTACGTGATGAGGAGATCTGG---TC--GGTGGATGACACGGT
1 TCCTACGTGATGAGGAGATCTGGTTATCTAGG-GG-TGACACGAC
* * *
598560 TCTTATGTGATGAGGACG-GCTGGTTATCTAGGGGTGACAC-AGC
1 TCCTACGTGATGAGGA-GATCTGGTTATCTAGGGGTGACACGA-C
*
598603 TCCTACGTGATAAGGAGATCTGGTT
1 TCCTACGTGATGAGGAGATCTGGTT
598628 GGCTGAACAT
Statistics
Matches: 86, Mismatches: 11, Indels: 22
0.72 0.09 0.18
Matches are distributed among these distances:
38 2 0.02
39 2 0.02
40 27 0.31
41 1 0.01
42 3 0.03
43 47 0.55
44 2 0.02
45 2 0.02
ACGTcount: A:0.22, C:0.18, G:0.34, T:0.26
Consensus pattern (43 bp):
TCCTACGTGATGAGGAGATCTGGTTATCTAGGGGTGACACGAC
Found at i:598609 original size:83 final size:83
Alignment explanation
Indices: 598470--598626 Score: 262
Period size: 83 Copynumber: 1.9 Consensus size: 83
598460 AAGGTATATA
*
598470 ACACGGTTCCTACGTGATGAGGACGACTGGTTATCTAGGGGTGACACGACTCCTACGTGATGAGG
1 ACACGGTTCCTACGTGATGAGGACGACTGGTTATCTAGGGGTGACACGACTCCTACGTGATAAGG
598535 AGATCTGGTCGGTGGATG
66 AGATCTGGTCGGTGGATG
* * *
598553 ACACGGTTCTTATGTGATGAGGACGGCTGGTTATCTAGGGGTGACAC-AGCTCCTACGTGATAAG
1 ACACGGTTCCTACGTGATGAGGACGACTGGTTATCTAGGGGTGACACGA-CTCCTACGTGATAAG
598617 GAGATCTGGT
65 GAGATCTGGT
598627 TGGCTGAACA
Statistics
Matches: 69, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
82 1 0.01
83 68 0.99
ACGTcount: A:0.22, C:0.18, G:0.34, T:0.25
Consensus pattern (83 bp):
ACACGGTTCCTACGTGATGAGGACGACTGGTTATCTAGGGGTGACACGACTCCTACGTGATAAGG
AGATCTGGTCGGTGGATG
Found at i:599592 original size:6 final size:6
Alignment explanation
Indices: 599581--599656 Score: 82
Period size: 6 Copynumber: 12.3 Consensus size: 6
599571 TTTTTATTTA
* *
599581 TTTTTC TTTTTC TTTTCTT TTTTTC CTTTTC TTTTTC TTTTTC TTTTT-
1 TTTTTC TTTTTC TTTT-TC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
* *
599629 TTCTTTT TTTTTC TTTTTTC TTCTTC TT
1 TT-TTTC TTTTTC -TTTTTC TTTTTC TT
599657 CAAGTGTAAT
Statistics
Matches: 60, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
5 2 0.03
6 45 0.75
7 13 0.22
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTTC
Found at i:599619 original size:31 final size:31
Alignment explanation
Indices: 599588--599656 Score: 63
Period size: 31 Copynumber: 2.2 Consensus size: 31
599578 TTATTTTTCT
* *
599588 TTTTCTTTTCTTTTTTTCCTTTTCTTTTTCT-
1 TTTTCTTTTC-TTTTTTCTTTTTCTTTTTTTC
*
599619 TTTTCTTTT-TTTCTTTTTTTTTC-TTTTTTC
1 TTTTCTTTTCTTT-TTTCTTTTTCTTTTTTTC
599649 TTCTTCTT
1 TT-TTCTT
599657 CAAGTGTAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
29 8 0.25
30 10 0.31
31 14 0.44
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (31 bp):
TTTTCTTTTCTTTTTTCTTTTTCTTTTTTTC
Found at i:599650 original size:25 final size:26
Alignment explanation
Indices: 599582--599646 Score: 109
Period size: 25 Copynumber: 2.6 Consensus size: 26
599572 TTTTATTTAT
599582 TTTTCTTTTTC-TTTTCTTTTTTTCC
1 TTTTCTTTTTCTTTTTCTTTTTTTCC
599607 TTTTCTTTTTCTTTTTCTTTTTTT-C
1 TTTTCTTTTTCTTTTTCTTTTTTTCC
599632 TTTT-TTTTTCTTTTT
1 TTTTCTTTTTCTTTTT
599647 TCTTCTTCTT
Statistics
Matches: 39, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
24 11 0.28
25 16 0.41
26 12 0.31
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (26 bp):
TTTTCTTTTTCTTTTTCTTTTTTTCC
Found at i:606895 original size:30 final size:29
Alignment explanation
Indices: 606861--606931 Score: 97
Period size: 30 Copynumber: 2.4 Consensus size: 29
606851 TTAAATTTGA
*
606861 ATGCATATTATTGGTAATGCGTTATAAATG
1 ATGCAT-TTATTGGTAATGCATTATAAATG
*
606891 ATGCATTTCATTGGTGATGCATTATAAATG
1 ATGCATTT-ATTGGTAATGCATTATAAATG
*
606921 ATGAATTTATT
1 ATGCATTTATT
606932 TATGTATAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
29 5 0.14
30 32 0.86
ACGTcount: A:0.32, C:0.07, G:0.18, T:0.42
Consensus pattern (29 bp):
ATGCATTTATTGGTAATGCATTATAAATG
Found at i:610569 original size:16 final size:18
Alignment explanation
Indices: 610529--610570 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 18
610519 TATGATTTTT
610529 ATTTTGAA-AAATTTACA
1 ATTTTGAATAAATTTACA
610546 ATTTTGAATAAATTTA-A
1 ATTTTGAATAAATTTACA
610563 A-TTTGAAT
1 ATTTTGAAT
610571 TGGAAGGGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.29
17 10 0.42
18 7 0.29
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.45
Consensus pattern (18 bp):
ATTTTGAATAAATTTACA
Found at i:612242 original size:12 final size:12
Alignment explanation
Indices: 612210--612235 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
612200 GCAAAGGGGT
612210 TTCTTTTCTCTC
1 TTCTTTTCTCTC
612222 TTCTTTTCTCTC
1 TTCTTTTCTCTC
612234 TT
1 TT
612236 TTGTTCTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (12 bp):
TTCTTTTCTCTC
Found at i:612947 original size:22 final size:23
Alignment explanation
Indices: 612920--612970 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 23
612910 ACTGGCCGAC
* * *
612920 AAAAAATGTAATTATTA-TAATA
1 AAAAAATATAATAATAATTAATA
612942 AAAAAATATAATAATAATTAATA
1 AAAAAATATAATAATAATTAATA
612965 AAAAAA
1 AAAAAA
612971 AACCCGTACA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
22 14 0.56
23 11 0.44
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (23 bp):
AAAAAATATAATAATAATTAATA
Found at i:614497 original size:57 final size:58
Alignment explanation
Indices: 614431--614545 Score: 223
Period size: 57 Copynumber: 2.0 Consensus size: 58
614421 TAGTAAGACT
614431 TTCTTTGTTAATAGGGATGTCAAGTTCCTTGAGCATGTTTTT-CCTTTAAGATGTCTA
1 TTCTTTGTTAATAGGGATGTCAAGTTCCTTGAGCATGTTTTTCCCTTTAAGATGTCTA
614488 TTCTTTGTTAATAGGGATGTCAAGTTCCTTGAGCATGTTTTTCCCTTTAAGATGTCTA
1 TTCTTTGTTAATAGGGATGTCAAGTTCCTTGAGCATGTTTTTCCCTTTAAGATGTCTA
614546 GTCCTCCAAA
Statistics
Matches: 57, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
57 42 0.74
58 15 0.26
ACGTcount: A:0.21, C:0.15, G:0.19, T:0.45
Consensus pattern (58 bp):
TTCTTTGTTAATAGGGATGTCAAGTTCCTTGAGCATGTTTTTCCCTTTAAGATGTCTA
Found at i:614591 original size:18 final size:19
Alignment explanation
Indices: 614555--614596 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
614545 AGTCCTCCAA
* *
614555 ATTCTCCTTTTTTTTCCTG
1 ATTCTCCTTTTTGTGCCTG
*
614574 TTTCTCC-TTTTGTGCCTG
1 ATTCTCCTTTTTGTGCCTG
614592 ATTCT
1 ATTCT
614597 GAATTTCTTG
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.05, C:0.26, G:0.10, T:0.60
Consensus pattern (19 bp):
ATTCTCCTTTTTGTGCCTG
Found at i:616617 original size:2 final size:2
Alignment explanation
Indices: 616610--616639 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
616600 AGCGAAAAGG
616610 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
616640 GTTTAACCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:619843 original size:42 final size:43
Alignment explanation
Indices: 619773--619857 Score: 163
Period size: 42 Copynumber: 2.0 Consensus size: 43
619763 TTTAAATATA
619773 AAAATTGAAATCCTCTCTTTCTCTCATATCGTTTTTATTTATT
1 AAAATTGAAATCCTCTCTTTCTCTCATATCGTTTTTATTTATT
619816 AAAATTGAAAT-CTCTCTTTCTCTCATATCGTTTTTATTTATT
1 AAAATTGAAATCCTCTCTTTCTCTCATATCGTTTTTATTTATT
619858 TACTTGTAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
42 31 0.74
43 11 0.26
ACGTcount: A:0.26, C:0.18, G:0.05, T:0.52
Consensus pattern (43 bp):
AAAATTGAAATCCTCTCTTTCTCTCATATCGTTTTTATTTATT
Found at i:622403 original size:56 final size:56
Alignment explanation
Indices: 622341--622483 Score: 166
Period size: 56 Copynumber: 2.6 Consensus size: 56
622331 TTTTTACAGG
* * *
622341 TTATTATTCTAACAAGAGTTTATTGTCATTAGACATACAACTAAGCAAAAA-CATGA
1 TTATTATTCTAACAAGAGTTTATTGTCATCACACATACAACTAAACAAAAATC-TGA
* * * *
622397 TTATTATT-TCAACAAGAGTTTATTGTCATCACACGTACAAGTAAATAAAAATCTGG
1 TTATTATTCT-AACAAGAGTTTATTGTCATCACACATACAACTAAACAAAAATCTGA
*
622453 TTATTATTTCGAAC-AGAGTTTATTGTCATCA
1 TTATTA-TTCTAACAAGAGTTTATTGTCATCA
622484 TATATTGGAG
Statistics
Matches: 75, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
55 1 0.01
56 68 0.91
57 6 0.08
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.36
Consensus pattern (56 bp):
TTATTATTCTAACAAGAGTTTATTGTCATCACACATACAACTAAACAAAAATCTGA
Found at i:624524 original size:24 final size:24
Alignment explanation
Indices: 624478--624540 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 24
624468 TTCACATATA
* *
624478 ATTTGAAAT-ATAGTTAATATAAT
1 ATTTAAAATAATAATTAATATAAT
*
624501 ATTTAAAATAATAATTAATTTAAT
1 ATTTAAAATAATAATTAATATAAT
*
624525 ATGTATAAA-AATAATT
1 ATTTA-AAATAATAATT
624541 TCATATTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
23 8 0.24
24 23 0.68
25 3 0.09
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (24 bp):
ATTTAAAATAATAATTAATATAAT
Found at i:624574 original size:19 final size:19
Alignment explanation
Indices: 624530--624582 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
624520 TTAATATGTA
*
624530 TAAAAATAATTTCATATTT
1 TAAAAATAATTTCAAATTT
**
624549 TTCAAATAAATTT-AAATTT
1 TAAAAAT-AATTTCAAATTT
624568 TAAAAATTAATTTCA
1 TAAAAA-TAATTTCA
624583 TCAAAGATTT
Statistics
Matches: 26, Mismatches: 5, Indels: 5
0.72 0.14 0.14
Matches are distributed among these distances:
19 19 0.73
20 7 0.27
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (19 bp):
TAAAAATAATTTCAAATTT
Found at i:624648 original size:26 final size:26
Alignment explanation
Indices: 624617--624679 Score: 67
Period size: 26 Copynumber: 2.4 Consensus size: 26
624607 ACTATATTTA
624617 TTTTTTATATAA-TCAAAGT-ATAATT
1 TTTTTTATATAACT-AAAGTAATAATT
* * *
624642 TTATTTTTTTTAACTTAAGTAATAATT
1 TT-TTTTATATAACTAAAGTAATAATT
624669 TTTTTTATATA
1 TTTTTTATATA
624680 TTATTTCTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
25 2 0.07
26 19 0.63
27 9 0.30
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.59
Consensus pattern (26 bp):
TTTTTTATATAACTAAAGTAATAATT
Found at i:626239 original size:21 final size:22
Alignment explanation
Indices: 626215--626256 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
626205 TATAGTGTTA
626215 TATTTATACTATAA-TATATAT
1 TATTTATACTATAAGTATATAT
*
626236 TATTTATATTATAAGTATATA
1 TATTTATACTATAAGTATATA
626257 GTATATATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (22 bp):
TATTTATACTATAAGTATATAT
Found at i:626271 original size:29 final size:28
Alignment explanation
Indices: 626195--626277 Score: 82
Period size: 29 Copynumber: 2.9 Consensus size: 28
626185 TACATATATC
* *
626195 ATATAGTTTATATAGTGTTATATT-T-AT
1 ATATAGTATATAT-GTATTATATTATAAT
*
626222 ACTATAATATATAT-TATTTATATTATAAGT
1 A-TATAGTATATATGTA-TTATATTATAA-T
626252 ATATAGTATATATGTATTATATTATA
1 ATATAGTATATATGTATTATATTATA
626278 CAATATACAT
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
26 1 0.02
27 8 0.17
28 11 0.24
29 22 0.48
30 4 0.09
ACGTcount: A:0.40, C:0.01, G:0.07, T:0.52
Consensus pattern (28 bp):
ATATAGTATATATGTATTATATTATAAT
Found at i:627137 original size:31 final size:30
Alignment explanation
Indices: 627079--627142 Score: 74
Period size: 31 Copynumber: 2.1 Consensus size: 30
627069 AGTTACGTCG
*
627079 GGGACCATACTGCAAACAGAATGAATGTTGA
1 GGGACCATACTGCAAACAGAATAAATGTT-A
* ** *
627110 GGGACCATATTGCAAATGGACTAAATGTTA
1 GGGACCATACTGCAAACAGAATAAATGTTA
627140 GGG
1 GGG
627143 GATTATATTG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
30 4 0.14
31 24 0.86
ACGTcount: A:0.36, C:0.14, G:0.28, T:0.22
Consensus pattern (30 bp):
GGGACCATACTGCAAACAGAATAAATGTTA
Found at i:627808 original size:31 final size:31
Alignment explanation
Indices: 627769--627839 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
627759 CTTTTAAAAC
627769 TTGCAATATAATCCC-CTAACATTTAGTCCGT
1 TTGCAATATAATCCCTC-AACATTTAGTCCGT
* ** *
627800 TTGTAATATGGTCCCTCAACATTTAGTCCTT
1 TTGCAATATAATCCCTCAACATTTAGTCCGT
627831 TTGCAATAT
1 TTGCAATAT
627840 GGTCCCCGAC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
31 33 0.97
32 1 0.03
ACGTcount: A:0.27, C:0.23, G:0.11, T:0.39
Consensus pattern (31 bp):
TTGCAATATAATCCCTCAACATTTAGTCCGT
Found at i:627840 original size:31 final size:30
Alignment explanation
Indices: 627782--627845 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 30
627772 CAATATAATC
*
627782 CCCTAACATTTAGTCCGTTTGTAATATGGT
1 CCCTAACATTTAGTCCGTTTGCAATATGGT
*
627812 CCCTCAACATTTAGTCCTTTTGCAATATGGT
1 CCCT-AACATTTAGTCCGTTTGCAATATGGT
627843 CCC
1 CCC
627846 CGACGTAACT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 4 0.13
31 27 0.87
ACGTcount: A:0.22, C:0.27, G:0.14, T:0.38
Consensus pattern (30 bp):
CCCTAACATTTAGTCCGTTTGCAATATGGT
Found at i:628196 original size:17 final size:17
Alignment explanation
Indices: 628174--628206 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
628164 CAAAACCATA
*
628174 ATATTATTTTTTATATT
1 ATATTATATTTTATATT
628191 ATATTATATTTTATAT
1 ATATTATATTTTATAT
628207 AAATAAACAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
ATATTATATTTTATATT
Found at i:628567 original size:167 final size:167
Alignment explanation
Indices: 628318--628625 Score: 571
Period size: 167 Copynumber: 1.8 Consensus size: 167
628308 TTAAAAAATC
*
628318 ATAAATTTTTATTCAACTATTTATAATCTAATACTAAAATTTAACTTTAAAAAACATATATAAAA
1 ATAAATTTTTATTCAACTATTTATAATCTAATAATAAAATTTAACTTTAAAAAACATATATAAAA
628383 ATATATAATTTAATAAAATATGCATTCAACTAATTTATATCACTTTAATCAAGTACTATAATTTT
66 ATATATAATTTAATAAAATATGCATTCAACTAATTTATATCACTTTAATCAAGTACTATAATTTT
*
628448 ATATTCTTATTTAAATAGTATGACAATTAAATTTTTT
131 ACATTCTTATTTAAATAGTATGACAATTAAATTTTTT
*
628485 ATAAATTTTTATTCAACTATTTATAATCTAATAATAAAATTTAATTTTAAAAAACATATATAAAA
1 ATAAATTTTTATTCAACTATTTATAATCTAATAATAAAATTTAACTTTAAAAAACATATATAAAA
* *
628550 ATATATAATTTAATAAAATATGCGTTCAACTAATTTATATCGCTTTAATCAAGTACTATAATTTT
66 ATATATAATTTAATAAAATATGCATTCAACTAATTTATATCACTTTAATCAAGTACTATAATTTT
628615 ACATTCTTATT
131 ACATTCTTATT
628626 AAACAAGATA
Statistics
Matches: 136, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
167 136 1.00
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.44
Consensus pattern (167 bp):
ATAAATTTTTATTCAACTATTTATAATCTAATAATAAAATTTAACTTTAAAAAACATATATAAAA
ATATATAATTTAATAAAATATGCATTCAACTAATTTATATCACTTTAATCAAGTACTATAATTTT
ACATTCTTATTTAAATAGTATGACAATTAAATTTTTT
Found at i:631512 original size:16 final size:16
Alignment explanation
Indices: 631491--631537 Score: 94
Period size: 16 Copynumber: 2.9 Consensus size: 16
631481 ATTCTAAATT
631491 TTTTCGAGTTCAAGTC
1 TTTTCGAGTTCAAGTC
631507 TTTTCGAGTTCAAGTC
1 TTTTCGAGTTCAAGTC
631523 TTTTCGAGTTCAAGT
1 TTTTCGAGTTCAAGT
631538 TTCAATATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.19, C:0.17, G:0.19, T:0.45
Consensus pattern (16 bp):
TTTTCGAGTTCAAGTC
Found at i:631604 original size:26 final size:26
Alignment explanation
Indices: 631524--631591 Score: 127
Period size: 26 Copynumber: 2.6 Consensus size: 26
631514 GTTCAAGTCT
631524 TTTCGAGTTCAAGTTTCAATATTATA
1 TTTCGAGTTCAAGTTTCAATATTATA
*
631550 TTTCGAGTTCGAGTTTCAATATTATA
1 TTTCGAGTTCAAGTTTCAATATTATA
631576 TTTCGAGTTCAAGTTT
1 TTTCGAGTTCAAGTTT
631592 AACTTGATAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.26, C:0.12, G:0.15, T:0.47
Consensus pattern (26 bp):
TTTCGAGTTCAAGTTTCAATATTATA
Found at i:631928 original size:21 final size:20
Alignment explanation
Indices: 631903--631945 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
631893 TCCGGTTTTC
* *
631903 AAAACACTGATAAAATGACTA
1 AAAACACCGAAAAAATGA-TA
*
631924 AAAACGCCGAAAAAATGATA
1 AAAACACCGAAAAAATGATA
631944 AA
1 AA
631946 TGTGCTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.60, C:0.14, G:0.12, T:0.14
Consensus pattern (20 bp):
AAAACACCGAAAAAATGATA
Found at i:635956 original size:98 final size:99
Alignment explanation
Indices: 635773--636005 Score: 265
Period size: 98 Copynumber: 2.3 Consensus size: 99
635763 GATAAGTTTT
* * * * *
635773 ATTCTTGGGTTTTATTTGGATTTAAAATATAATGATTTAGGTTTTAGGGTTTTTGATATACTGTT
1 ATTCTTGGGATTTATTTGGATTTAACATACAATCATTTAGGTTTTAAGG---TTGATATACTGTT
** * *
635838 GATTTTCTGGAATATTAAGTTATT-GTACGCTTAGTTC
63 GATTTTCTAAAATATTAAGTT-TTCATAAGCTTAGTTC
* *
635875 ATTCTTGGGGTTTCTTTGGATTTAACATACAA-CATTTTAGGTTTTAAGG-TGATATACTGTTGA
1 ATTCTTGGGATTTATTTGGATTTAACATACAATCA-TTTAGGTTTTAAGGTTGATATACTGTTGA
* *
635938 TTTTCTAAAATATTAAGTTTTCATAAGTTTAGTTT
65 TTTTCTAAAATATTAAGTTTTCATAAGCTTAGTTC
* *
635973 ATTCTTGTGATTTGTTTGGATTTAACATACAAT
1 ATTCTTGGGATTTATTTGGATTTAACATACAAT
636006 GTTATAACTT
Statistics
Matches: 113, Mismatches: 15, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
97 2 0.02
98 69 0.61
101 1 0.01
102 41 0.36
ACGTcount: A:0.26, C:0.07, G:0.18, T:0.49
Consensus pattern (99 bp):
ATTCTTGGGATTTATTTGGATTTAACATACAATCATTTAGGTTTTAAGGTTGATATACTGTTGAT
TTTCTAAAATATTAAGTTTTCATAAGCTTAGTTC
Found at i:638791 original size:22 final size:20
Alignment explanation
Indices: 638759--638805 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 20
638749 GTTGAATATA
638759 TTGTTCCATACTATTATGGT
1 TTGTTCCATACTATTATGGT
*
638779 TTGTGTCCTATACTATTGTGGT
1 TTGT-TCC-ATACTATTATGGT
638801 TTGTT
1 TTGTT
638806 GAATATATTG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 4 0.17
21 4 0.17
22 16 0.67
ACGTcount: A:0.15, C:0.13, G:0.19, T:0.53
Consensus pattern (20 bp):
TTGTTCCATACTATTATGGT
Found at i:641997 original size:138 final size:136
Alignment explanation
Indices: 641822--642211 Score: 414
Period size: 139 Copynumber: 2.8 Consensus size: 136
641812 CAAGTGTAGG
* * *
641822 ATCTAATATTAA-CCTAATTAA-TTTAATCAATTATTGAATCAAATATTTGAAATGGAACCTCAG
1 ATCTAATATTAATCCTAATCAATTTTAATCAATTATTGAATCGAATAATTGAAATGGAACCTCAG
* * *
641885 GCTTAAATGCAAGGACCAAAT-AAAATATTCTCTTAAATTAAGGGA-TAAAATTATAATTAAACT
66 GCATAAA-GCAAGGACCAAATCAAAA-ATTCTCCTAAATTAAGGGACTAAAATGA-AATTAAACT
*
641948 AAAATAGAGGT
128 -AAATAGA-AT
* * * ** *
641959 -TCTAATATTAATCCTAACCAATTTTAGTTAATTATTGAATCGAGCAATTGAAATGGAACCATGA
1 ATCTAATATTAATCCTAATCAATTTTAATCAATTATTGAATCGAATAATTGAAATGGAACC-TCA
* * * * *
642023 -GCATAAAGGCTAGGACCAAATCAAAAATCCACCTAAATTAAGGGACTAAAGTGAAATTAATCTA
65 GGCATAAA-GCAAGGACCAAATCAAAAATTCTCCTAAATTAAGGGACTAAAATGAAATTAAACTA
*
642087 AATTGAAT
129 AATAGAAT
* *
642095 ACTCTAATTATTAATCCTAATCAGTTCTAATCAATTATTGAATCGAATAATTGAAATGGAACCTC
1 A-TCTAA-TATTAATCCTAATCAATTTTAATCAATTATTGAATCGAATAATTGAAATGGAACCTC
* * * * *
642160 GGGCATAAAGCTGATGACAAAATCAAGAATTCTCCTAAATTAAGGGACTAAA
64 AGGCATAAAGC-AAGGACCAAATCAAAAATTCTCCTAAATTAAGGGACTAAA
642212 TTTAAAGAAA
Statistics
Matches: 208, Mismatches: 35, Indels: 18
0.80 0.13 0.07
Matches are distributed among these distances:
136 12 0.06
137 13 0.06
138 82 0.39
139 101 0.49
ACGTcount: A:0.44, C:0.14, G:0.13, T:0.30
Consensus pattern (136 bp):
ATCTAATATTAATCCTAATCAATTTTAATCAATTATTGAATCGAATAATTGAAATGGAACCTCAG
GCATAAAGCAAGGACCAAATCAAAAATTCTCCTAAATTAAGGGACTAAAATGAAATTAAACTAAA
TAGAAT
Found at i:642247 original size:25 final size:26
Alignment explanation
Indices: 642219--642271 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 26
642209 AAATTTAAAG
*
642219 AAACCAAAATTTAAA-GGCCAAACCT
1 AAACCAAAACTTAAAGGGCCAAACCT
*
642244 AAACCTAAACTTAAAGGGCCAAACCT
1 AAACCAAAACTTAAAGGGCCAAACCT
642270 AA
1 AA
642272 GTGTTAATTG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 13 0.52
26 12 0.48
ACGTcount: A:0.51, C:0.25, G:0.09, T:0.15
Consensus pattern (26 bp):
AAACCAAAACTTAAAGGGCCAAACCT
Found at i:644302 original size:16 final size:13
Alignment explanation
Indices: 644275--644316 Score: 84
Period size: 13 Copynumber: 3.2 Consensus size: 13
644265 TTCCACACAA
644275 TTCTCCCTTCTTC
1 TTCTCCCTTCTTC
644288 TTCTCCCTTCTTC
1 TTCTCCCTTCTTC
644301 TTCTCCCTTCTTC
1 TTCTCCCTTCTTC
644314 TTC
1 TTC
644317 CTCCTCCCCG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (13 bp):
TTCTCCCTTCTTC
Found at i:645625 original size:22 final size:22
Alignment explanation
Indices: 645594--645639 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
645584 CATATACAGT
645594 ATACAGAGGTCCTTC-AGGACAA
1 ATACAGAGGTCCTTCGA-GACAA
* *
645616 ATACATAGGTCTTTCGAGACAA
1 ATACAGAGGTCCTTCGAGACAA
645638 AT
1 AT
645640 TTTACGTGCC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 20 0.95
23 1 0.05
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.24
Consensus pattern (22 bp):
ATACAGAGGTCCTTCGAGACAA
Found at i:646489 original size:21 final size:21
Alignment explanation
Indices: 646463--646503 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
646453 CAATGTTTTT
646463 GTGCATCGGTACACTATAGCA
1 GTGCATCGGTACACTATAGCA
* *
646484 GTGCATTGGTACACTGTAGC
1 GTGCATCGGTACACTATAGC
646504 GCTGTTCACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (21 bp):
GTGCATCGGTACACTATAGCA
Found at i:646559 original size:19 final size:19
Alignment explanation
Indices: 646535--646585 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 19
646525 TACTGTTCAC
* **
646535 AGTACTGTTCATACCGTAT
1 AGTACTATTCATACAATAT
646554 AGTACTATTCATACAATAT
1 AGTACTATTCATACAATAT
646573 AGTACTATTCATA
1 AGTACTATTCATA
646586 AAAACGTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.35, C:0.18, G:0.10, T:0.37
Consensus pattern (19 bp):
AGTACTATTCATACAATAT
Found at i:647079 original size:44 final size:44
Alignment explanation
Indices: 646902--647085 Score: 167
Period size: 44 Copynumber: 4.2 Consensus size: 44
646892 TGGAATTGAA
* *
646902 CAAAAGGGTGAAATTGATCCAATTTCTTATGTGATAGAATCAAG
1 CAAAAGGGTGATATTGATCCAACTTCTTATGTGATAGAATCAAG
* * * * * * *
646946 CGAAATGGTAATGCTT-ATCCAACTCCTTAGGTGAT-GTAATCGAG
1 CAAAAGGGTGAT-ATTGATCCAACTTCTTATGTGATAG-AATCAAG
* * * ** * *
646990 AAAAATGGTGATGTTGATCCAAC-TCTTTATGTGACGGACTTAAG
1 CAAAAGGGTGATATTGATCCAACTTC-TTATGTGATAGAATCAAG
*
647034 CAAAAGGGTGATATTGATCCAACTTCTTATGTAATAGAATCAAG
1 CAAAAGGGTGATATTGATCCAACTTCTTATGTGATAGAATCAAG
647078 CAAAAGGG
1 CAAAAGGG
647086 AATGTAGATC
Statistics
Matches: 107, Mismatches: 27, Indels: 12
0.73 0.18 0.08
Matches are distributed among these distances:
43 4 0.04
44 98 0.92
45 5 0.05
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (44 bp):
CAAAAGGGTGATATTGATCCAACTTCTTATGTGATAGAATCAAG
Found at i:654227 original size:16 final size:16
Alignment explanation
Indices: 654206--654239 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
654196 GGCTTCTAAG
654206 TTTGTTTAAATACTCT
1 TTTGTTTAAATACTCT
654222 TTTGTTTAAATACTCT
1 TTTGTTTAAATACTCT
654238 TT
1 TT
654240 GGATCAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.24, C:0.12, G:0.06, T:0.59
Consensus pattern (16 bp):
TTTGTTTAAATACTCT
Found at i:654499 original size:19 final size:19
Alignment explanation
Indices: 654475--654514 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
654465 ATCTTAGATA
*
654475 GGGGTATCGGTACCCTCTG
1 GGGGTATCGATACCCTCTG
654494 GGGGTATCGATACCCTCTG
1 GGGGTATCGATACCCTCTG
654513 GG
1 GG
654515 CAATCTGCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.12, C:0.25, G:0.38, T:0.25
Consensus pattern (19 bp):
GGGGTATCGATACCCTCTG
Found at i:654915 original size:19 final size:17
Alignment explanation
Indices: 654877--654911 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
654867 TTATTACTCC
654877 CCCTTACTATAACACTT
1 CCCTTACTATAACACTT
654894 CCCTTACTATAACACTT
1 CCCTTACTATAACACTT
654911 C
1 C
654912 TCCCCCTTTT
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:0.29, C:0.37, G:0.00, T:0.34
Consensus pattern (17 bp):
CCCTTACTATAACACTT
Found at i:656643 original size:13 final size:13
Alignment explanation
Indices: 656627--656651 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
656617 TTGAAAAACT
656627 ATGTTTGAAAATA
1 ATGTTTGAAAATA
656640 ATGTTTGAAAAT
1 ATGTTTGAAAAT
656652 CAATATATAG
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:0.44, C:0.00, G:0.16, T:0.40
Consensus pattern (13 bp):
ATGTTTGAAAATA
Found at i:657193 original size:22 final size:22
Alignment explanation
Indices: 657122--657193 Score: 74
Period size: 22 Copynumber: 3.2 Consensus size: 22
657112 CCCGTGGAGA
* *
657122 GTATCGGTACCC-TCACATGTGG
1 GTATCGGTACCCAT-ACAAGAGG
* *
657144 TTATCGGTACCCATTCAAAGAGG
1 GTATCGGTACCCATAC-AAGAGG
*
657167 GTATCGGTACCCATACAAGGGG
1 GTATCGGTACCCATACAAGAGG
657189 GTATC
1 GTATC
657194 AATACCTAGC
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
22 22 0.54
23 19 0.46
ACGTcount: A:0.25, C:0.24, G:0.26, T:0.25
Consensus pattern (22 bp):
GTATCGGTACCCATACAAGAGG
Found at i:657199 original size:22 final size:23
Alignment explanation
Indices: 657151--657199 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 23
657141 TGGTTATCGG
* **
657151 TACCCATTCAAAGAGGGTATCGG
1 TACCCATACAAAGAGGGTATCAA
*
657174 TACCCATAC-AAGGGGGTATCAA
1 TACCCATACAAAGAGGGTATCAA
657196 TACC
1 TACC
657200 TAGCGCTTAG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.33, C:0.24, G:0.22, T:0.20
Consensus pattern (23 bp):
TACCCATACAAAGAGGGTATCAA
Found at i:661330 original size:11 final size:10
Alignment explanation
Indices: 661294--661430 Score: 59
Period size: 11 Copynumber: 13.1 Consensus size: 10
661284 CATTTTTTTC
661294 TCTTTCTCTTT
1 TCTTT-TCTTT
661305 CTCCTTTTCTTT
1 -T-CTTTTCTTT
661317 TCTTTTCATTT
1 TCTTTTC-TTT
*
661328 TCTGTTTTTTTT
1 TC--TTTTCTTT
* *
661340 TCCTTTCTTC
1 TCTTTTCTTT
661350 T-TTTTCTTT
1 TCTTTTCTTT
661359 TC--TTCTTT
1 TCTTTTCTTT
661367 TCTCTTTCTGTT
1 TCT-TTTCT-TT
*
661379 TTTTTTCTATT
1 TCTTTTCT-TT
*
661390 TATTTT-TTT
1 TCTTTTCTTT
* * *
661399 CCTCTACGTTT
1 TCTTTTC-TTT
661410 TCTTTTTCTTT
1 TC-TTTTCTTT
*
661421 T-TATTCTTT
1 TCTTTTCTTT
661430 T
1 T
661431 TTATTCTCTT
Statistics
Matches: 96, Mismatches: 17, Indels: 27
0.69 0.12 0.19
Matches are distributed among these distances:
8 8 0.08
9 19 0.20
10 13 0.14
11 30 0.31
12 18 0.19
13 8 0.08
ACGTcount: A:0.04, C:0.20, G:0.02, T:0.74
Consensus pattern (10 bp):
TCTTTTCTTT
Found at i:661374 original size:14 final size:14
Alignment explanation
Indices: 661291--661375 Score: 72
Period size: 14 Copynumber: 6.1 Consensus size: 14
661281 TCTCATTTTT
661291 TTCTCTTTCTCTTTC
1 TTCT-TTTCTCTTTC
*
661306 TCCTTTTCT-TTTC
1 TTCTTTTCTCTTTC
*
661319 TTTTCATTTTCTGTTT-
1 --TTC-TTTTCTCTTTC
661335 TT-TTTTC-CTTTC
1 TTCTTTTCTCTTTC
661347 TTCTTTT-TCTTTTC
1 TTCTTTTCTC-TTTC
661361 TTCTTTTCTCTTTC
1 TTCTTTTCTCTTTC
661375 T
1 T
661376 GTTTTTTTTC
Statistics
Matches: 58, Mismatches: 3, Indels: 19
0.73 0.04 0.24
Matches are distributed among these distances:
11 3 0.05
12 7 0.12
13 9 0.16
14 23 0.40
15 7 0.12
16 6 0.10
17 3 0.05
ACGTcount: A:0.01, C:0.25, G:0.01, T:0.73
Consensus pattern (14 bp):
TTCTTTTCTCTTTC
Found at i:661381 original size:14 final size:13
Alignment explanation
Indices: 661287--661381 Score: 60
Period size: 14 Copynumber: 7.5 Consensus size: 13
661277 CATCTCTCAT
661287 TTTTTTCTCTTTC
1 TTTTTTCTCTTTC
*
661300 -TCTTTCTCCTTT-
1 TTTTTTCT-CTTTC
*
661312 TCTTTTCT-TTTC
1 TTTTTTCTCTTTC
* *
661324 -ATTTTCTGTTT-
1 TTTTTTCTCTTTC
661335 TTTTTTC-CTTTC
1 TTTTTTCTCTTTC
661347 TTCTTTT-TCTTTTC
1 TT-TTTTCTC-TTTC
661361 TTCTTTTCTCTTTC
1 TT-TTTTCTCTTTC
661375 TGTTTTT
1 T-TTTTT
661382 TTTCTATTTA
Statistics
Matches: 65, Mismatches: 6, Indels: 21
0.71 0.07 0.23
Matches are distributed among these distances:
11 12 0.18
12 16 0.25
13 14 0.22
14 20 0.31
15 3 0.05
ACGTcount: A:0.01, C:0.22, G:0.02, T:0.75
Consensus pattern (13 bp):
TTTTTTCTCTTTC
Found at i:661384 original size:45 final size:47
Alignment explanation
Indices: 661286--661384 Score: 134
Period size: 45 Copynumber: 2.1 Consensus size: 47
661276 TCATCTCTCA
661286 TTTTTTTCTCTTTCTCTTTCTCCTTTTCTTTTCTTTTCATTTTCTGTT
1 TTTTTTTCTCTTTCTCTTTCTCCTTTTC-TTTCTTTTCATTTTCTGTT
*
661334 TTTTTTTC-CTTTCTTCTTT-TTCTTTTC-TTCTTTTC-TCTTTCTGTT
1 TTTTTTTCTCTTTC-TCTTTCTCCTTTTCTTTCTTTTCAT-TTTCTGTT
661379 TTTTTT
1 TTTTTT
661385 CTATTTATTT
Statistics
Matches: 48, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
44 1 0.02
45 22 0.46
47 12 0.25
48 13 0.27
ACGTcount: A:0.01, C:0.21, G:0.02, T:0.76
Consensus pattern (47 bp):
TTTTTTTCTCTTTCTCTTTCTCCTTTTCTTTCTTTTCATTTTCTGTT
Found at i:661386 original size:56 final size:57
Alignment explanation
Indices: 661291--661397 Score: 139
Period size: 56 Copynumber: 1.9 Consensus size: 57
661281 TCTCATTTTT
*
661291 TTCTCTTTCTCTTTCTCCTTTTCTTTTCTTTTCATTTTCTGTTT-TTTTTTCCTTTC
1 TTCTCTTTCTCTTTCTCCTTTTCTTTTCTTTTCATTTTCTATTTATTTTTTCCTTTC
* * *
661347 TTCTTTTTCT-TTTCTTCTTTTCTCTTTCTGTTT-TTTTTCTATTTATTTTTT
1 TTCTCTTTCTCTTTCTCCTTTTCT-TTTCT-TTTCATTTTCTATTTATTTTTT
661398 TCCTCTACGT
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
55 12 0.27
56 23 0.52
57 9 0.20
ACGTcount: A:0.03, C:0.21, G:0.02, T:0.75
Consensus pattern (57 bp):
TTCTCTTTCTCTTTCTCCTTTTCTTTTCTTTTCATTTTCTATTTATTTTTTCCTTTC
Found at i:661418 original size:6 final size:6
Alignment explanation
Indices: 661288--661422 Score: 64
Period size: 6 Copynumber: 21.8 Consensus size: 6
661278 ATCTCTCATT
* * *
661288 TTTTTC TCTTTCTC TTTCTC CTTTTC -TTTTC -TTTTC ATTTTC TGTTTT-
1 TTTTTC T-TTT-TC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC T-TTTTC
* *
661336 TTTTTCC TTTCTTC TTTTTC -TTTTC TTCTTTTC TCTTTC TGTTT- TTTTTC
1 TTTTT-C TTT-TTC TTTTTC TTTTTC -T-TTTTC TTTTTC TTTTTC TTTTTC
* * * * *
661386 TATTTATT TTTTTC CTCTAC GTTTTC TTTTTC TTTTT
1 T-TTT-TC TTTTTC TTTTTC TTTTTC TTTTTC TTTTT
661423 ATTCTTTTTT
Statistics
Matches: 100, Mismatches: 16, Indels: 26
0.70 0.11 0.18
Matches are distributed among these distances:
5 23 0.23
6 42 0.42
7 23 0.23
8 12 0.12
ACGTcount: A:0.03, C:0.21, G:0.02, T:0.74
Consensus pattern (6 bp):
TTTTTC
Found at i:661427 original size:15 final size:15
Alignment explanation
Indices: 661347--661431 Score: 50
Period size: 15 Copynumber: 5.5 Consensus size: 15
661337 TTTTCCTTTC
*
661347 TTCTTTTTC-TTTTC
1 TTCTTTTTCTTTTTA
* *
661361 TTCTTTTCTCTTTCTG
1 TTCTTTT-TCTTTTTA
* *
661377 TTTTTTTTCTATTTA
1 TTCTTTTTCTTTTTA
*
661392 TT-TTTTTCCTCTACGTT-
1 TTCTTTTT-CT-T--TTTA
661409 TTCTTTTTCTTTTTA
1 TTCTTTTTCTTTTTA
661424 TTCTTTTT
1 TTCTTTTT
661432 TATTCTCTTA
Statistics
Matches: 54, Mismatches: 9, Indels: 15
0.69 0.12 0.19
Matches are distributed among these distances:
14 14 0.26
15 19 0.35
16 10 0.19
17 4 0.07
18 7 0.13
ACGTcount: A:0.05, C:0.18, G:0.02, T:0.75
Consensus pattern (15 bp):
TTCTTTTTCTTTTTA
Found at i:667904 original size:22 final size:21
Alignment explanation
Indices: 667862--667901 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
667852 AAGACTATTT
667862 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTGAAATA
**
667883 TCATTTTTGTATTTTGAAA
1 TCATTTTTCAATTTTGAAA
667902 ATAAAGTCTT
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:0.30, C:0.07, G:0.07, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTGAAATA
Found at i:669873 original size:20 final size:20
Alignment explanation
Indices: 669848--669887 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
669838 ATCTTACATA
669848 GGGTATCGATACCCTCTGGG
1 GGGTATCGATACCCTCTGGG
*
669868 GGGTATCGGTACCCTCTGGG
1 GGGTATCGATACCCTCTGGG
669888 CAATCTGCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.12, C:0.25, G:0.38, T:0.25
Consensus pattern (20 bp):
GGGTATCGATACCCTCTGGG
Found at i:672480 original size:2 final size:2
Alignment explanation
Indices: 672473--672549 Score: 145
Period size: 2 Copynumber: 38.5 Consensus size: 2
672463 TGGACCACCA
672473 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
672515 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
672550 ACTCACCAAT
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 73 1.00
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (2 bp):
AT
Found at i:676297 original size:21 final size:22
Alignment explanation
Indices: 676264--676321 Score: 73
Period size: 21 Copynumber: 2.6 Consensus size: 22
676254 TAGTGCTCTA
* *
676264 TATTTAATATTTATAGTGTTTAT
1 TATTT-ATATTTATAATGCTTAT
676287 TATTT-TATTTATAATGCTTAT
1 TATTTATATTTATAATGCTTAT
*
676308 TATTTATATATATA
1 TATTTATATTTATA
676322 TATATATATT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 19 0.61
22 7 0.23
23 5 0.16
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (22 bp):
TATTTATATTTATAATGCTTAT
Found at i:683567 original size:21 final size:21
Alignment explanation
Indices: 683541--683582 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
683531 CTATATTTAA
* *
683541 TATTTATAGTGTTTATTATTT
1 TATTTATAATGCTTATTATTT
683562 TATTTATAATGCTTATTATTT
1 TATTTATAATGCTTATTATTT
683583 ATATATATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.02, G:0.07, T:0.64
Consensus pattern (21 bp):
TATTTATAATGCTTATTATTT
Found at i:688014 original size:42 final size:41
Alignment explanation
Indices: 687958--688172 Score: 177
Period size: 40 Copynumber: 5.2 Consensus size: 41
687948 CGATTTAAGC
* *
687958 ACAAATGCCTCTAAATACTCGTACTTTAGTGGCATTTTTTAT
1 ACAAACGCCACTAAATACTCGTACTTTAGTGGC-TTTTTTAT
* *
688000 ATAAATGCCACTAAATACT-GTACTTTAGTGG-TGTTTTTAT
1 ACAAACGCCACTAAATACTCGTACTTTAGTGGCT-TTTTTAT
** * * * * *
688040 ACAAACGCGGGCTGAAGACTTGTAATTTAGTGGTTTTTTTTTAT
1 ACAAACGC-CACTAAATACTCGTACTTTAGTGG--CTTTTTTAT
* * * *
688084 ATAAACGCCACTAAAT-GTTGTACTTTAGTGGCGTTTTTAT
1 ACAAACGCCACTAAATACTCGTACTTTAGTGGCTTTTTTAT
* * * * *
688124 ACAGACGACGCTAAAGACTCATACTTTAGTGGC-TTTTTAT
1 ACAAACGCCACTAAATACTCGTACTTTAGTGGCTTTTTTAT
688164 ACAAACGCC
1 ACAAACGCC
688173 GCAATTTATC
Statistics
Matches: 138, Mismatches: 28, Indels: 16
0.76 0.15 0.09
Matches are distributed among these distances:
39 1 0.01
40 45 0.33
41 32 0.23
42 41 0.30
43 4 0.03
44 14 0.10
45 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.38
Consensus pattern (41 bp):
ACAAACGCCACTAAATACTCGTACTTTAGTGGCTTTTTTAT
Found at i:688161 original size:84 final size:84
Alignment explanation
Indices: 687968--688161 Score: 243
Period size: 84 Copynumber: 2.3 Consensus size: 84
687958 ACAAATGCCT
* * *
687968 CTAAATACTCGTACTTTAGTGGC--ATTTTTTATATAAATGCCACTAAATACTGTACTTTAGTGG
1 CTAAAGACTCGTACTTTAGTGGCTTTTTTTTTATATAAACGCCACTAAATACTGTACTTTAGTGG
*
688031 TGTTTTTATACAAACGCGGG
66 CGTTTTTATACAAACGC-GG
* * * **
688051 CTGAAGACTTGTAATTTAGTGG-TTTTTTTTTATATAAACGCCACTAAATGTTGTACTTTAGTGG
1 CTAAAGACTCGTACTTTAGTGGCTTTTTTTTTATATAAACGCCACTAAATACTGTACTTTAGTGG
*
688115 CGTTTTTATACAGACGAC-G
66 CGTTTTTATACAAACG-CGG
*
688134 CTAAAGACTCATACTTTAGTGGCTTTTT
1 CTAAAGACTCGTACTTTAGTGGCTTTTT
688162 ATACAAACGC
Statistics
Matches: 93, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
83 37 0.40
84 55 0.59
85 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.18, T:0.40
Consensus pattern (84 bp):
CTAAAGACTCGTACTTTAGTGGCTTTTTTTTTATATAAACGCCACTAAATACTGTACTTTAGTGG
CGTTTTTATACAAACGCGG
Found at i:689065 original size:25 final size:23
Alignment explanation
Indices: 689037--689086 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 23
689027 GGTTTATTTG
689037 ATATAATATTAATAA-TTTATTAAAA
1 ATATAATA-TAA-AAGTTTA-TAAAA
*
689062 ATATATTATAAAAGTTTATAAAA
1 ATATAATATAAAAGTTTATAAAA
689085 AT
1 AT
689087 TATGTAGGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 9 0.39
24 7 0.30
25 7 0.30
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (23 bp):
ATATAATATAAAAGTTTATAAAA
Found at i:689617 original size:5 final size:5
Alignment explanation
Indices: 689607--689633 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
689597 GTTCGGGTTT
689607 TTCGG TTCGG TTCGG TTCGG TTCGG TT
1 TTCGG TTCGG TTCGG TTCGG TTCGG TT
689634 TATCGGTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.00, C:0.19, G:0.37, T:0.44
Consensus pattern (5 bp):
TTCGG
Found at i:689617 original size:19 final size:19
Alignment explanation
Indices: 689564--689621 Score: 77
Period size: 18 Copynumber: 3.2 Consensus size: 19
689554 AAACCGAAAC
689564 CGGGTTTTTCGGTTCGGTT
1 CGGGTTTTTCGGTTCGGTT
*
689583 C-GGTTTTT--TTTACGGTT
1 CGGGTTTTTCGGTT-CGGTT
689600 CGGGTTTTTCGGTTCGGTT
1 CGGGTTTTTCGGTTCGGTT
689619 CGG
1 CGG
689622 TTCGGTTCGG
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
16 2 0.06
17 6 0.18
18 14 0.42
19 9 0.27
20 2 0.06
ACGTcount: A:0.02, C:0.16, G:0.34, T:0.48
Consensus pattern (19 bp):
CGGGTTTTTCGGTTCGGTT
Found at i:697252 original size:9 final size:9
Alignment explanation
Indices: 697216--697252 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
697206 TATTAGAAGA
697216 TATTTTATT
1 TATTTTATT
* *
697225 AATTTTAAT
1 TATTTTATT
697234 TATTTTATT
1 TATTTTATT
697243 TATTTTATT
1 TATTTTATT
697252 T
1 T
697253 TGCATTCAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (9 bp):
TATTTTATT
Found at i:697593 original size:18 final size:20
Alignment explanation
Indices: 697558--697594 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
697548 TTTTTATAAC
*
697558 TATATATAAATATTATTAAT
1 TATATATAAATATAATTAAT
697578 TATAT-TAAATA-AATTAA
1 TATATATAAATATAATTAA
697595 AATTATACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 5 0.31
19 6 0.38
20 5 0.31
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TATATATAAATATAATTAAT
Found at i:697852 original size:12 final size:13
Alignment explanation
Indices: 697830--697858 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
697820 GTCGATTCTC
697830 TTTTCTCTTTGTT
1 TTTTCTCTTTGTT
697843 TTTTCT-TTTGTT
1 TTTTCTCTTTGTT
697855 TTTT
1 TTTT
697859 AATAAGAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.00, C:0.10, G:0.07, T:0.83
Consensus pattern (13 bp):
TTTTCTCTTTGTT
Found at i:698421 original size:21 final size:21
Alignment explanation
Indices: 698360--698421 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
698350 CTTGATAAAA
698360 TTAAATTTTAAATTAATT-TT
1 TTAAATTTTAAATTAATTATT
* * *
698380 TATACATATTAAATTTATTATT
1 T-TAAATTTTAAATTAATTATT
*
698402 TTAAATTTTATATTAATTAT
1 TTAAATTTTAAATTAATTAT
698422 ATTTTAAAAA
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
20 1 0.03
21 29 0.88
22 3 0.09
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (21 bp):
TTAAATTTTAAATTAATTATT
Found at i:700016 original size:64 final size:64
Alignment explanation
Indices: 699884--700022 Score: 185
Period size: 64 Copynumber: 2.2 Consensus size: 64
699874 TGCACTAAGG
** * **
699884 GTGCATCGATGCATAAAATGCATTCGATGTTTCAAACAAGTCTGGGTGTATCGATGCATGGTCT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTCAAACAAACCTGAGTGTATCGATGCATGGTAA
699948 GTGCATCGATGCATAAAATGCATTCGATGTTTTCATAA-AAACCTGAGTGCT-TCGATGCATGG-
1 GTGCATCGATGCATAAAATGCATTCGATG-TTTCA-AACAAACCTGAGTG-TATCGATGCATGGT
700010 AA
63 AA
700012 GTGCATCGATG
1 GTGCATCGATG
700023 TATGGAAGTG
Statistics
Matches: 67, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
64 40 0.60
65 24 0.36
66 3 0.04
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.30
Consensus pattern (64 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTCAAACAAACCTGAGTGTATCGATGCATGGTAA
Found at i:700020 original size:18 final size:18
Alignment explanation
Indices: 699993--700061 Score: 120
Period size: 18 Copynumber: 3.8 Consensus size: 18
699983 TAAAAACCTG
*
699993 AGTGCTTCGATGCATGGA
1 AGTGCATCGATGCATGGA
*
700011 AGTGCATCGATGTATGGA
1 AGTGCATCGATGCATGGA
700029 AGTGCATCGATGCATGGA
1 AGTGCATCGATGCATGGA
700047 AGTGCATCGATGCAT
1 AGTGCATCGATGCAT
700062 AAAATGCATT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 48 1.00
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (18 bp):
AGTGCATCGATGCATGGA
Found at i:700074 original size:18 final size:18
Alignment explanation
Indices: 699999--700070 Score: 74
Period size: 18 Copynumber: 4.1 Consensus size: 18
699989 CCTGAGTGCT
* *
699999 TCGATGCATGGAAGTGCA
1 TCGATGCATGAAAATGCA
* * *
700017 TCGATGTATGGAAGTGCA
1 TCGATGCATGAAAATGCA
* *
700035 TCGATGCATGGAAGTGCA
1 TCGATGCATGAAAATGCA
700053 TCGATGCAT-AAAATGCA
1 TCGATGCATGAAAATGCA
700070 T
1 T
700071 TCGAAATGGT
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
17 7 0.14
18 43 0.86
ACGTcount: A:0.31, C:0.15, G:0.29, T:0.25
Consensus pattern (18 bp):
TCGATGCATGAAAATGCA
Found at i:702701 original size:23 final size:23
Alignment explanation
Indices: 702673--702754 Score: 82
Period size: 23 Copynumber: 3.6 Consensus size: 23
702663 GCATGGCATT
702673 GTGCATCGATGCACATTCAAGGA
1 GTGCATCGATGCACATTCAAGGA
* *
702696 GTGCATCGGTGCATC-TTC-ATGA
1 GTGCATCGATGCA-CATTCAAGGA
*
702718 -TGTATCGATGCACATTCAATGG-
1 GTGCATCGATGCACATTCAA-GGA
702740 GATGCATCGATGCAC
1 G-TGCATCGATGCAC
702755 TATGCACAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 11
0.73 0.09 0.17
Matches are distributed among these distances:
20 1 0.02
21 13 0.28
22 4 0.09
23 16 0.34
24 13 0.28
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.27
Consensus pattern (23 bp):
GTGCATCGATGCACATTCAAGGA
Found at i:703123 original size:21 final size:22
Alignment explanation
Indices: 703083--703123 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
703073 CTAAAGGTTT
* *
703083 TGTAAAGATATCCGCTAATTGG
1 TGTAAAGATATCAGCAAATTGG
703105 TGTAAAG-TATCAGCAAATT
1 TGTAAAGATATCAGCAAATT
703124 CTAGAACAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.32
Consensus pattern (22 bp):
TGTAAAGATATCAGCAAATTGG
Found at i:708125 original size:36 final size:35
Alignment explanation
Indices: 708079--708202 Score: 126
Period size: 36 Copynumber: 3.4 Consensus size: 35
708069 TAAAAACCTG
*
708079 AGTGGATCGATGCATGGAAGTGCATCGATGCATAGA
1 AGTGCATCGATGCATGGAAGTGCATCGATGCATA-A
*
708115 AGTGCATCGATGCATAGAAGTGCATCGATGCATAA
1 AGTGCATCGATGCATGGAAGTGCATCGATGCATAA
* * *
708150 AATGCATTCGA--AATGGTGAGTGCATCGATGCATCAA
1 AGTGCA-TCGATGCATGG-AAGTGCATCGATGCAT-AA
*
708186 TGAGTGCATCGGTGCAT
1 --AGTGCATCGATGCAT
708203 TCATTCACGA
Statistics
Matches: 72, Mismatches: 9, Indels: 11
0.78 0.10 0.12
Matches are distributed among these distances:
34 3 0.04
35 21 0.29
36 38 0.53
37 3 0.04
38 5 0.07
39 2 0.03
ACGTcount: A:0.31, C:0.16, G:0.29, T:0.24
Consensus pattern (35 bp):
AGTGCATCGATGCATGGAAGTGCATCGATGCATAA
Found at i:708160 original size:18 final size:18
Alignment explanation
Indices: 708079--708148 Score: 122
Period size: 18 Copynumber: 3.9 Consensus size: 18
708069 TAAAAACCTG
* *
708079 AGTGGATCGATGCATGGA
1 AGTGCATCGATGCATAGA
708097 AGTGCATCGATGCATAGA
1 AGTGCATCGATGCATAGA
708115 AGTGCATCGATGCATAGA
1 AGTGCATCGATGCATAGA
708133 AGTGCATCGATGCATA
1 AGTGCATCGATGCATA
708149 AAATGCATTC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 50 1.00
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.23
Consensus pattern (18 bp):
AGTGCATCGATGCATAGA
Found at i:716124 original size:45 final size:46
Alignment explanation
Indices: 716060--716164 Score: 151
Period size: 45 Copynumber: 2.3 Consensus size: 46
716050 TGCACTAAGG
*
716060 GTGCATCGATGCATAAAATGCATTCAATG-TTTCA-AACAAGCCTGA
1 GTGCATCGATGCATAAAATGCATTCAATGTTTTCATAA-AAACCTGA
* * *
716105 GTGCATCGTTGCATAAAATGCATTCGATGTTTTCATAAAAACTTGA
1 GTGCATCGATGCATAAAATGCATTCAATGTTTTCATAAAAACCTGA
716151 GTGCATCGATGCAT
1 GTGCATCGATGCAT
716165 GGAAGTGCAT
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
45 27 0.51
46 24 0.45
47 2 0.04
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.30
Consensus pattern (46 bp):
GTGCATCGATGCATAAAATGCATTCAATGTTTTCATAAAAACCTGA
Found at i:716195 original size:18 final size:18
Alignment explanation
Indices: 716152--716191 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
716142 AAAACTTGAG
* *
716152 TGCATCGATGCATGGAAG
1 TGCATCGATGCATGAAAA
716170 TGCATCGATGCAT-AAAA
1 TGCATCGATGCATGAAAA
716187 TGCAT
1 TGCAT
716192 TCGAAATGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (18 bp):
TGCATCGATGCATGAAAA
Found at i:720636 original size:41 final size:41
Alignment explanation
Indices: 720591--720699 Score: 119
Period size: 41 Copynumber: 2.7 Consensus size: 41
720581 AAAAACTCTT
* *
720591 ACTTTAGTGGCCTTTGTATACAAACGCCGCTACAGACTCAG
1 ACTTTAGTGGCATTTGTATACAAACGCCGCTACAAACTCAG
* * * * * *
720632 ACTTTAGTGGCGTTTGTATATAAACGGCGCTATAAATTCAT
1 ACTTTAGTGGCATTTGTATACAAACGCCGCTACAAACTCAG
* * *
720673 ACGTTAGTGGTATTTTTATACAAACGC
1 ACTTTAGTGGCATTTGTATACAAACGC
720700 TATTATATAC
Statistics
Matches: 55, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
41 55 1.00
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.33
Consensus pattern (41 bp):
ACTTTAGTGGCATTTGTATACAAACGCCGCTACAAACTCAG
Found at i:720756 original size:41 final size:41
Alignment explanation
Indices: 720676--720761 Score: 120
Period size: 41 Copynumber: 2.1 Consensus size: 41
720666 AATTCATACG
*
720676 TTAGTGGTATTTTTATACAAACGCTATTATATACGCGTACT
1 TTAGTGGTATTTTTATACAAACGCTATTATAGACGCGTACT
* * *
720717 TTAGTGGTGTTTTTATACAAACGCTGTTGA-AGACTCGTACT
1 TTAGTGGTATTTTTATACAAACGCTATT-ATAGACGCGTACT
720758 TTAG
1 TTAG
720762 GAAACGCATC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
41 39 0.98
42 1 0.03
ACGTcount: A:0.27, C:0.14, G:0.19, T:0.41
Consensus pattern (41 bp):
TTAGTGGTATTTTTATACAAACGCTATTATAGACGCGTACT
Done.