Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167882.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_15, 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: 22478863
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 61000 characters in sequence are not A, C, G, or T
File 4 of 106
Found at i:509280 original size:22 final size:22
Alignment explanation
Indices: 509255--509495 Score: 181
Period size: 22 Copynumber: 11.1 Consensus size: 22
509245 GACAGGATTG
* *
509255 TGAATCCTCAAATAAGAATATT
1 TGAATTCTCAAATAAGAATCTT
509277 TGAATT-TCAAATGAA-AATCTT
1 TGAATTCTCAAAT-AAGAATCTT
* *
509298 TGAATTTTCAAATAAAAATCTT
1 TGAATTCTCAAATAAGAATCTT
* *
509320 TGAGTTCTCAAATGAGAATCTT
1 TGAATTCTCAAATAAGAATCTT
* *
509342 TGAGTTCTCAAATGAGAATCTT
1 TGAATTCTCAAATAAGAATCTT
* * * * *
509364 TGAGTTTTTAAATGAGAATTTT
1 TGAATTCTCAAATAAGAATCTT
* * *
509386 TGAGTT-TTAAATGAGAA-CTT
1 TGAATTCTCAAATAAGAATCTT
* *
509406 TGAGTTATCAAATGAAG-ATCTT
1 TGAATTCTCAAAT-AAGAATCTT
* *
509428 TGAGTTTTCAAATGAAG-ATCTT
1 TGAATTCTCAAAT-AAGAATCTT
* * *
509450 TGAGTTTTCAAATAAGAATATT
1 TGAATTCTCAAATAAGAATCTT
**
509472 TGAGCT-TCAAATAAGAATCTT
1 TGAATTCTCAAATAAGAATCTT
509493 TGA
1 TGA
509496 GATGTGAAAC
Statistics
Matches: 196, Mismatches: 16, Indels: 15
0.86 0.07 0.07
Matches are distributed among these distances:
20 8 0.04
21 56 0.29
22 132 0.67
ACGTcount: A:0.37, C:0.09, G:0.15, T:0.39
Consensus pattern (22 bp):
TGAATTCTCAAATAAGAATCTT
Found at i:509353 original size:44 final size:43
Alignment explanation
Indices: 509262--509496 Score: 262
Period size: 44 Copynumber: 5.4 Consensus size: 43
509252 TTGTGAATCC
* * * *
509262 TCAAATAAGAATATTTGA-ATTTCAAATGAAAATCTTTGAATTT
1 TCAAATAAGAATCTTTGAGTTTTCAAATGAGAATCTTTG-AGTT
* *
509305 TCAAATAAAAATCTTTGAGTTCTCAAATGAGAATCTTTGAGTT
1 TCAAATAAGAATCTTTGAGTTTTCAAATGAGAATCTTTGAGTT
* * *
509348 CTCAAATGAGAATCTTTGAGTTTTTAAATGAGAATTTTTGAGTT
1 -TCAAATAAGAATCTTTGAGTTTTCAAATGAGAATCTTTGAGTT
* * *
509392 TTAAATGAGAA-CTTTGAGTTATCAAATGA-AGATCTTTGAGTTT
1 TCAAATAAGAATCTTTGAGTTTTCAAATGAGA-ATCTTTGAG-TT
* * *
509435 TCAAATGAAG-ATCTTTGAGTTTTCAAATAAGAATATTTGAGCT
1 TCAAAT-AAGAATCTTTGAGTTTTCAAATGAGAATCTTTGAGTT
509478 TCAAATAAGAATCTTTGAG
1 TCAAATAAGAATCTTTGAG
509497 ATGTGAAACC
Statistics
Matches: 163, Mismatches: 21, Indels: 16
0.81 0.10 0.08
Matches are distributed among these distances:
41 1 0.01
42 27 0.17
43 53 0.33
44 81 0.50
45 1 0.01
ACGTcount: A:0.37, C:0.09, G:0.15, T:0.39
Consensus pattern (43 bp):
TCAAATAAGAATCTTTGAGTTTTCAAATGAGAATCTTTGAGTT
Found at i:509420 original size:86 final size:87
Alignment explanation
Indices: 509261--509496 Score: 282
Period size: 86 Copynumber: 2.7 Consensus size: 87
509251 ATTGTGAATC
* * * * * * *
509261 CTCAAATAAGAATATTTGA-ATTTCAAATGAAAATCTTTGAATTTTCAAATAAAAATCTTTGAGT
1 CTCAAATGAGAATCTTTGAGTTTTCAAATGAGAATATTTGAGTTTT-AAATAAGAATCTTTGAGT
*
509325 TCTCAAATG-AGAATCTTTGAGTT
65 TATCAAATGAAG-ATCTTTGAGTT
* * *
509348 CTCAAATGAGAATCTTTGAGTTTTTAAATGAGAATTTTTGAGTTTTAAATGAGAA-CTTTGAGTT
1 CTCAAATGAGAATCTTTGAGTTTTCAAATGAGAATATTTGAGTTTTAAATAAGAATCTTTGAGTT
509412 ATCAAATGAAGATCTTTGAGTT
66 ATCAAATGAAGATCTTTGAGTT
* * * *
509434 TTCAAATGA-AGATCTTTGAGTTTTCAAATAAGAATATTTGAGCTTCAAATAAGAATCTTTGAG
1 CTCAAATGAGA-ATCTTTGAGTTTTCAAATGAGAATATTTGAGTTTTAAATAAGAATCTTTGAG
509497 ATGTGAAACC
Statistics
Matches: 128, Mismatches: 17, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
85 1 0.01
86 73 0.57
87 33 0.26
88 21 0.16
ACGTcount: A:0.37, C:0.09, G:0.15, T:0.39
Consensus pattern (87 bp):
CTCAAATGAGAATCTTTGAGTTTTCAAATGAGAATATTTGAGTTTTAAATAAGAATCTTTGAGTT
ATCAAATGAAGATCTTTGAGTT
Found at i:510004 original size:16 final size:17
Alignment explanation
Indices: 509976--510014 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 17
509966 ATTTTACAAA
509976 TGTGAATTTTGAAATCT
1 TGTGAATTTTGAAATCT
*
509993 TGTGAA-TTTGAATTCT
1 TGTGAATTTTGAAATCT
510009 TGTGAA
1 TGTGAA
510015 GCTGAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 15 0.71
17 6 0.29
ACGTcount: A:0.28, C:0.05, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTTTGAAATCT
Found at i:510160 original size:18 final size:18
Alignment explanation
Indices: 510120--510160 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
510110 AAGGTTTTTA
*
510120 TGAATTTGAAAATTGTAG
1 TGAATTTGAAAATTCTAG
* *
510138 CGAATTTGAAAATTCTTG
1 TGAATTTGAAAATTCTAG
510156 TGAAT
1 TGAAT
510161 CTTTGAATTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.37, C:0.05, G:0.20, T:0.39
Consensus pattern (18 bp):
TGAATTTGAAAATTCTAG
Found at i:510179 original size:15 final size:15
Alignment explanation
Indices: 510156--510190 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
510146 AAAATTCTTG
*
510156 TGAATCTTTGAATTA
1 TGAACCTTTGAATTA
*
510171 TGAACCTTTGAATTT
1 TGAACCTTTGAATTA
510186 TGAAC
1 TGAAC
510191 TCAAATTGTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.31, C:0.11, G:0.14, T:0.43
Consensus pattern (15 bp):
TGAACCTTTGAATTA
Found at i:510319 original size:44 final size:42
Alignment explanation
Indices: 510241--510325 Score: 116
Period size: 44 Copynumber: 2.0 Consensus size: 42
510231 TATTGTTGAG
* *
510241 GAGCTTTATTTATTTTCAAAGTTATTGAGCCTCTGATTAGAA
1 GAGCTTTATTTATTTTCAAAGTCATGGAGCCTCTGATTAGAA
* *
510283 GAGCTTTATTTATTTTCTCAAAGTCGTGGAGCCTCTGTTTAGA
1 GAGCTTTATTTA-TTT-TCAAAGTCATGGAGCCTCTGATTAGA
510326 GGAGTTTTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
42 12 0.32
43 3 0.08
44 22 0.59
ACGTcount: A:0.25, C:0.14, G:0.19, T:0.42
Consensus pattern (42 bp):
GAGCTTTATTTATTTTCAAAGTCATGGAGCCTCTGATTAGAA
Found at i:513698 original size:14 final size:15
Alignment explanation
Indices: 513679--513708 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
513669 TTGACTTTTT
513679 TCTTTTT-TTTTTAA
1 TCTTTTTGTTTTTAA
513693 TCTTTTTGTTTTTAA
1 TCTTTTTGTTTTTAA
513708 T
1 T
513709 TTAATAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.13, C:0.07, G:0.03, T:0.77
Consensus pattern (15 bp):
TCTTTTTGTTTTTAA
Found at i:514088 original size:46 final size:46
Alignment explanation
Indices: 514030--514125 Score: 129
Period size: 46 Copynumber: 2.1 Consensus size: 46
514020 TAATTGATAC
* * *** *
514030 AATACTAAAAACCTTGATAAAGATGTGAGCTTTTGTTATTGAACCA
1 AATAATAAAAACCTTGACAAAGATACAAACTTTTGTTATTGAACCA
*
514076 AATAATAAAAACCTTGACAAAGATACAAACTTTTGTTATTGAGCCA
1 AATAATAAAAACCTTGACAAAGATACAAACTTTTGTTATTGAACCA
514122 AATA
1 AATA
514126 TTTTGATATT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.44, C:0.14, G:0.12, T:0.30
Consensus pattern (46 bp):
AATAATAAAAACCTTGACAAAGATACAAACTTTTGTTATTGAACCA
Found at i:515038 original size:20 final size:20
Alignment explanation
Indices: 515013--515052 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
515003 TTTCTTGAGC
* *
515013 TTCTAAGTTTTTAGATTTGA
1 TTCTAAGATTTAAGATTTGA
515033 TTCTAAGATTTAAGATTTGA
1 TTCTAAGATTTAAGATTTGA
515053 ATTTGAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.30, C:0.05, G:0.15, T:0.50
Consensus pattern (20 bp):
TTCTAAGATTTAAGATTTGA
Found at i:515541 original size:12 final size:12
Alignment explanation
Indices: 515524--515574 Score: 52
Period size: 11 Copynumber: 4.4 Consensus size: 12
515514 AGGTTCTCCT
515524 TTTTTTTGTTTA
1 TTTTTTTGTTTA
*
515536 -TTTTTTGCTT-
1 TTTTTTTGTTTA
**
515546 TGATTTTGTTTA
1 TTTTTTTGTTTA
*
515558 TTTTTATGTTTA
1 TTTTTTTGTTTA
515570 TTTTT
1 TTTTT
515575 GTTTTTTATA
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
11 16 0.53
12 14 0.47
ACGTcount: A:0.10, C:0.02, G:0.10, T:0.78
Consensus pattern (12 bp):
TTTTTTTGTTTA
Found at i:515575 original size:22 final size:23
Alignment explanation
Indices: 515526--515578 Score: 76
Period size: 22 Copynumber: 2.4 Consensus size: 23
515516 GTTCTCCTTT
515526 TTTTTGTTTATTTTTTGCTTTGA
1 TTTTTGTTTATTTTTTGCTTTGA
515549 -TTTTGTTTATTTTTATG-TTT-A
1 TTTTTGTTTATTTTT-TGCTTTGA
515570 TTTTTGTTT
1 TTTTTGTTT
515579 TTTATATATT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
21 1 0.04
22 25 0.89
23 2 0.07
ACGTcount: A:0.09, C:0.02, G:0.11, T:0.77
Consensus pattern (23 bp):
TTTTTGTTTATTTTTTGCTTTGA
Found at i:515593 original size:22 final size:22
Alignment explanation
Indices: 515549--515617 Score: 61
Period size: 22 Copynumber: 3.0 Consensus size: 22
515539 TTTGCTTTGA
* *
515549 TTTTGTTTATTTTTATGTTTAT
1 TTTTGTTTATTTATATATTTAT
515571 TTTTGTTT-TTTATATATTATAT
1 TTTTGTTTATTTATATATT-TAT
*
515593 TTATAGTTATATTT-TAATATTTAT
1 TT-TTGTT-TATTTAT-ATATTTAT
515617 T
1 T
515618 ATTTTAAATG
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
21 8 0.21
22 13 0.33
23 4 0.10
24 6 0.15
25 8 0.21
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.71
Consensus pattern (22 bp):
TTTTGTTTATTTATATATTTAT
Found at i:515762 original size:21 final size:21
Alignment explanation
Indices: 515738--515781 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
515728 GACTTTATTA
*
515738 ATTAATTGCATGATATTTTAT
1 ATTAATTGCATGATAATTTAT
515759 ATTAATTGCATGATAATTTAT
1 ATTAATTGCATGATAATTTAT
515780 AT
1 AT
515782 ATTATATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.36, C:0.05, G:0.09, T:0.50
Consensus pattern (21 bp):
ATTAATTGCATGATAATTTAT
Found at i:515838 original size:20 final size:21
Alignment explanation
Indices: 515813--515853 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
515803 TTATGTTATA
*
515813 ATATTATTGCATGATA-TATT
1 ATATTATTACATGATACTATT
515833 ATATTATTACATGATACTATT
1 ATATTATTACATGATACTATT
515854 TTGCATGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.49
Consensus pattern (21 bp):
ATATTATTACATGATACTATT
Found at i:516074 original size:38 final size:38
Alignment explanation
Indices: 515985--516086 Score: 102
Period size: 38 Copynumber: 2.7 Consensus size: 38
515975 AAAATATTTT
*
515985 TAAAAATTCTACCAATATA-TTGAAGGATAATACTTAA
1 TAAAAAATCTACCAATATATTTGAAGGATAATACTTAA
* * *
516022 TGAAAAGTCCTACCAATATATTTG-AGGATAAT-CTTCGA
1 TAAAAAAT-CTACCAATATATTTGAAGGATAATACTT-AA
* *
516060 TAAAAAATCTTACCAAGATATTGGAAG
1 TAAAAAATC-TACCAATATATTTGAAG
516087 ATATTTTTGA
Statistics
Matches: 53, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
37 10 0.19
38 38 0.72
39 5 0.09
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.30
Consensus pattern (38 bp):
TAAAAAATCTACCAATATATTTGAAGGATAATACTTAA
Found at i:518084 original size:23 final size:23
Alignment explanation
Indices: 518058--518101 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
518048 CATTTCCTGT
518058 AAGGTATACTTACATAGAAATAC
1 AAGGTATACTTACATAGAAATAC
518081 AAGGTATACTTACATAGAAAT
1 AAGGTATACTTACATAGAAAT
518102 GCCATCTGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.48, C:0.11, G:0.14, T:0.27
Consensus pattern (23 bp):
AAGGTATACTTACATAGAAATAC
Found at i:521728 original size:46 final size:43
Alignment explanation
Indices: 521673--521837 Score: 123
Period size: 46 Copynumber: 3.6 Consensus size: 43
521663 GTCTTTGAAT
521673 TTTTAGATGTGAAACTCTAAATTTTTTTAATGAGAACCTTTAAAAA
1 TTTTAGATGTGAAAC-CTAAATTTTTTTAATGAGAA-CTTT-AAAA
* * * * * *
521719 TTTTGGATGTGAAGCCATAAAGTTTTTGAAAGAGAACTTTTCAAA
1 TTTTAGATGTGAAACC-TAAATTTTTTTAATGAGAAC-TTTAAAA
** * * ** * *
521764 TTTCGGATGTGAATCTCTAAAATATTTCAAATGTGAATCTTTGAAA
1 TTTTAGATGTGAAAC-CT-AAATTTTTTTAATGAGAA-CTTTAAAA
521810 TTTTAGATGTGAATACCTAAATTTTTTT
1 TTTTAGATGTGAA-ACCTAAATTTTTTT
521838 GAAAGAAATT
Statistics
Matches: 92, Mismatches: 21, Indels: 13
0.73 0.17 0.10
Matches are distributed among these distances:
45 26 0.28
46 64 0.70
47 2 0.02
ACGTcount: A:0.35, C:0.09, G:0.15, T:0.41
Consensus pattern (43 bp):
TTTTAGATGTGAAACCTAAATTTTTTTAATGAGAACTTTAAAA
Found at i:521819 original size:22 final size:24
Alignment explanation
Indices: 521763--521823 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
521753 AACTTTTCAA
*
521763 ATTTCGGATGTGAATCTCTAAAAT
1 ATTTCAGATGTGAATCTCTAAAAT
* * *
521787 ATTTCAAATGTGAATCTTTGAAAT
1 ATTTCAGATGTGAATCTCTAAAAT
521811 -TTT-AGATGTGAAT
1 ATTTCAGATGTGAAT
521824 ACCTAAATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
22 9 0.28
23 3 0.09
24 20 0.62
ACGTcount: A:0.34, C:0.08, G:0.16, T:0.41
Consensus pattern (24 bp):
ATTTCAGATGTGAATCTCTAAAAT
Found at i:522107 original size:17 final size:18
Alignment explanation
Indices: 522093--522127 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
522083 CAAATCTTTC
522093 ATTATTGTGAATCTTTAA
1 ATTATTGTGAATCTTTAA
*
522111 ATTCTTGTGAAT-TTTAA
1 ATTATTGTGAATCTTTAA
522128 GTTCTTGCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.31, C:0.06, G:0.11, T:0.51
Consensus pattern (18 bp):
ATTATTGTGAATCTTTAA
Found at i:522132 original size:17 final size:18
Alignment explanation
Indices: 522097--522273 Score: 75
Period size: 17 Copynumber: 10.2 Consensus size: 18
522087 TCTTTCATTA
522097 TTGTGAATCTTTAAATTC
1 TTGTGAATCTTTAAATTC
*
522115 TTGTGAAT-TTTAAGTTC
1 TTGTGAATCTTTAAATTC
* * * *
522132 TTG-CAAACCTAAAATTC
1 TTGTGAATCTTTAAATTC
* * * *
522149 TTGTGAAAC-TGAATTTT
1 TTGTGAATCTTTAAATTC
*
522166 TTGTGAA-CTTGATAA-TC
1 TTGTGAATCTTTA-AATTC
*
522183 TTGCGAATCTTTAAGA--C
1 TTGTGAATCTTTAA-ATTC
*
522200 TTGTGAATCTTTAAAATC
1 TTGTGAATCTTTAAATTC
* * *
522218 ATTGAGAAAC-TAAAATTC
1 -TTGTGAATCTTTAAATTC
* * *
522236 TTATGAAT-TTGAAAATC
1 TTGTGAATCTTTAAATTC
* * *
522253 TTGTGAAACTCTGAATTC
1 TTGTGAATCTTTAAATTC
522271 TTG
1 TTG
522274 CATATCTTGT
Statistics
Matches: 118, Mismatches: 30, Indels: 22
0.69 0.18 0.13
Matches are distributed among these distances:
16 4 0.03
17 74 0.63
18 33 0.28
19 7 0.06
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.41
Consensus pattern (18 bp):
TTGTGAATCTTTAAATTC
Found at i:524009 original size:21 final size:20
Alignment explanation
Indices: 523978--524044 Score: 75
Period size: 21 Copynumber: 3.3 Consensus size: 20
523968 TCTTTTTTTT
523978 TTTTGTTTATTTTTTGCTTTGA
1 TTTT-TTTATTTTTTG-TTTGA
524000 TTTTTTTATTTTTATGTTTGA
1 TTTTTTTATTTTT-TGTTTGA
* *
524021 -TTTTAT-TTTTTTGTTTTA
1 TTTTTTTATTTTTTGTTTGA
524039 TTTTTT
1 TTTTTT
524045 ATATATTATA
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
18 6 0.15
19 9 0.22
20 5 0.12
21 14 0.35
22 6 0.15
ACGTcount: A:0.10, C:0.01, G:0.09, T:0.79
Consensus pattern (20 bp):
TTTTTTTATTTTTTGTTTGA
Found at i:524037 original size:13 final size:13
Alignment explanation
Indices: 523965--524044 Score: 67
Period size: 13 Copynumber: 6.2 Consensus size: 13
523955 AGGTTTTCCC
* *
523965 TTTTCTTTTTTTT
1 TTTTGTTTTATTT
523978 TTTTG-TTTA-TT
1 TTTTGTTTTATTT
*
523989 TTTTGCTTTGATTT
1 TTTTG-TTTTATTT
* *
524003 TTTTATTTT-TAT
1 TTTTGTTTTATTT
*
524015 GTTTGATTTTATTT
1 TTTTG-TTTTATTT
524029 TTTTGTTTTATTT
1 TTTTGTTTTATTT
524042 TTT
1 TTT
524045 ATATATTATA
Statistics
Matches: 52, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
11 7 0.13
12 8 0.15
13 25 0.48
14 12 0.23
ACGTcount: A:0.09, C:0.03, G:0.07, T:0.81
Consensus pattern (13 bp):
TTTTGTTTTATTT
Found at i:524080 original size:12 final size:13
Alignment explanation
Indices: 524036--524087 Score: 52
Period size: 12 Copynumber: 3.8 Consensus size: 13
524026 TTTTTTTGTT
*
524036 TTATTTTTTATATA
1 TTATATTTTA-ATA
*
524050 TTATATATT-ATA
1 TTATATTTTAATA
524062 TTATATTTTAATA
1 TTATATTTTAATA
524075 TTTATTATTTTAA
1 -TTA-TATTTTAA
524088 ATGGTTGATT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
12 11 0.34
13 3 0.09
14 10 0.31
15 8 0.25
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (13 bp):
TTATATTTTAATA
Found at i:524269 original size:28 final size:29
Alignment explanation
Indices: 524216--524281 Score: 80
Period size: 28 Copynumber: 2.2 Consensus size: 29
524206 TTGCATGATA
*
524216 ATTTATATATTATGTTATTACATGATATCTT
1 ATTT-TATATTA-GTTATTACATGATATATT
*
524247 ATTTTATATTA-TTATTTCATGATATATT
1 ATTTTATATTAGTTATTACATGATATATT
*
524275 ATATTAT
1 ATTTTAT
524282 TACATGATAC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 21 0.66
30 7 0.22
31 4 0.12
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.58
Consensus pattern (29 bp):
ATTTTATATTAGTTATTACATGATATATT
Found at i:524276 original size:15 final size:15
Alignment explanation
Indices: 524230--524276 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
524220 ATATATTATG
* *
524230 TTATTACATGATATC
1 TTATTTCATGATATA
*
524245 TTATTTTAT-AT-TA
1 TTATTTCATGATATA
524258 TTATTTCATGATATA
1 TTATTTCATGATATA
524273 TTAT
1 TTAT
524277 ATTATTACAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
13 9 0.35
14 4 0.15
15 13 0.50
ACGTcount: A:0.32, C:0.06, G:0.04, T:0.57
Consensus pattern (15 bp):
TTATTTCATGATATA
Found at i:524281 original size:20 final size:21
Alignment explanation
Indices: 524256--524295 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
524246 TATTTTATAT
*
524256 TATTATTTCATGATA-TATTA
1 TATTATTACATGATACTATTA
524276 TATTATTACATGATACTATT
1 TATTATTACATGATACTATT
524296 TTGCAAGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.35, C:0.07, G:0.05, T:0.53
Consensus pattern (21 bp):
TATTATTACATGATACTATTA
Found at i:524319 original size:14 final size:14
Alignment explanation
Indices: 524281--524325 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
524271 TATTATATTA
*
524281 TTACATGATACTATT
1 TTACATGATAAT-TT
* *
524296 TTGCAAGATAATTT
1 TTACATGATAATTT
524310 TTACATGATAATTT
1 TTACATGATAATTT
524324 TT
1 TT
524326 GTTTATTTTA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
14 16 0.64
15 9 0.36
ACGTcount: A:0.33, C:0.09, G:0.09, T:0.49
Consensus pattern (14 bp):
TTACATGATAATTT
Found at i:526129 original size:22 final size:21
Alignment explanation
Indices: 526104--526147 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
526094 TATTGTTAGA
* *
526104 ACTAATATTAATATTAAGATAT
1 ACTAAAATTAATA-TAAAATAT
*
526126 ACTAAAATTCATATAAAATAT
1 ACTAAAATTAATATAAAATAT
526147 A
1 A
526148 ATAACTAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.55, C:0.07, G:0.02, T:0.36
Consensus pattern (21 bp):
ACTAAAATTAATATAAAATAT
Found at i:540840 original size:16 final size:15
Alignment explanation
Indices: 540809--540850 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
540799 AATTTGTGAT
*
540809 TTTATT-TGATTTAA
1 TTTATTATGAATTAA
540823 TTTGATTATGAATTAA
1 TTT-ATTATGAATTAA
*
540839 TTTTTTATGAAT
1 TTTATTATGAAT
540851 GATTTCATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 3 0.12
15 11 0.46
16 10 0.42
ACGTcount: A:0.31, C:0.00, G:0.10, T:0.60
Consensus pattern (15 bp):
TTTATTATGAATTAA
Found at i:540999 original size:17 final size:18
Alignment explanation
Indices: 540967--541008 Score: 68
Period size: 17 Copynumber: 2.4 Consensus size: 18
540957 TAATTAAAAC
540967 ACTAAAATCGAAATTAAA
1 ACTAAAATCGAAATTAAA
*
540985 AGTAAAATC-AAATTAAA
1 ACTAAAATCGAAATTAAA
541002 ACTAAAA
1 ACTAAAA
541009 CTAAAACTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 14 0.64
18 8 0.36
ACGTcount: A:0.64, C:0.10, G:0.05, T:0.21
Consensus pattern (18 bp):
ACTAAAATCGAAATTAAA
Found at i:541034 original size:6 final size:6
Alignment explanation
Indices: 540998--541032 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
540988 AAAATCAAAT
* *
540998 TAAAAC TAAAAC TAAAAC TAAAAC CAAAAT TAAAA
1 TAAAAC TAAAAC TAAAAC TAAAAC TAAAAC TAAAA
541033 TTTTTAGACT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.69, C:0.14, G:0.00, T:0.17
Consensus pattern (6 bp):
TAAAAC
Found at i:541203 original size:3 final size:3
Alignment explanation
Indices: 541195--541352 Score: 123
Period size: 3 Copynumber: 54.7 Consensus size: 3
541185 GCCTGGCCTA
*
541195 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATG
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * * * * * **
541243 ATC ATC ATC ATC ATC ATC ATC ATT ATT ATT ATT ATT -TT AGG ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
** * *
541290 -TT ATT ATT ATT -TT AGG ATT -TT ATTT ATT ATT -TT GTT ATT ATC
1 ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT
*
541332 A-T ATT ATT ATT -TA ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT AT
541353 CTCTTGAAAA
Statistics
Matches: 131, Mismatches: 16, Indels: 16
0.80 0.10 0.10
Matches are distributed among these distances:
2 12 0.09
3 116 0.89
4 3 0.02
ACGTcount: A:0.31, C:0.05, G:0.04, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:541289 original size:11 final size:11
Alignment explanation
Indices: 541273--541308 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
541263 CATTATTATT
541273 ATTATTTTAGG
1 ATTATTTTAGG
**
541284 ATTATTTTATT
1 ATTATTTTAGG
541295 ATTATTTTAGG
1 ATTATTTTAGG
541306 ATT
1 ATT
541309 TTATTTATTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.11, T:0.61
Consensus pattern (11 bp):
ATTATTTTAGG
Found at i:541295 original size:22 final size:23
Alignment explanation
Indices: 541268--541320 Score: 90
Period size: 22 Copynumber: 2.3 Consensus size: 23
541258 ATCATCATTA
541268 TTATTATTATTTTAGGATTAT-T
1 TTATTATTATTTTAGGATTATAT
*
541290 TTATTATTATTTTAGGATTTTAT
1 TTATTATTATTTTAGGATTATAT
541313 TTATTATT
1 TTATTATT
541321 TTGTTATTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 20 0.69
23 9 0.31
ACGTcount: A:0.26, C:0.00, G:0.08, T:0.66
Consensus pattern (23 bp):
TTATTATTATTTTAGGATTATAT
Found at i:542199 original size:10 final size:11
Alignment explanation
Indices: 542174--542211 Score: 69
Period size: 11 Copynumber: 3.5 Consensus size: 11
542164 GCTAAGCCAC
542174 TTTTATTTTGG
1 TTTTATTTTGG
542185 TTTTATTTT-G
1 TTTTATTTTGG
542195 TTTTATTTTGG
1 TTTTATTTTGG
542206 TTTTAT
1 TTTTAT
542212 GTTTTTATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 10 0.38
11 16 0.62
ACGTcount: A:0.11, C:0.00, G:0.13, T:0.76
Consensus pattern (11 bp):
TTTTATTTTGG
Found at i:542228 original size:11 final size:11
Alignment explanation
Indices: 542174--542216 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
542164 GCTAAGCCAC
*
542174 TTTTATTTTGG
1 TTTTATTTTTG
542185 TTTTA-TTTTG
1 TTTTATTTTTG
*
542195 TTTTATTTTGG
1 TTTTATTTTTG
542206 TTTTATGTTTT
1 TTTTAT-TTTT
542217 TATTTTTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
10 9 0.33
11 15 0.56
12 3 0.11
ACGTcount: A:0.09, C:0.00, G:0.14, T:0.77
Consensus pattern (11 bp):
TTTTATTTTTG
Found at i:552811 original size:11 final size:11
Alignment explanation
Indices: 552795--552828 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
552785 ATTCCCAAAA
552795 TTTATTATTAT
1 TTTATTATTAT
552806 TTTATTATTAT
1 TTTATTATTAT
552817 TTT-TTATT-T
1 TTTATTATTAT
552826 TTT
1 TTT
552829 CTAAATTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 4 0.17
10 5 0.22
11 14 0.61
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTATTATTAT
Found at i:552864 original size:18 final size:18
Alignment explanation
Indices: 552843--552878 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
552833 ATTTAATCAT
552843 GAAAAAAAATACTAAGAA
1 GAAAAAAAATACTAAGAA
* *
552861 GAAAAAAACTATTAAGAA
1 GAAAAAAAATACTAAGAA
552879 AAATACTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.69, C:0.06, G:0.11, T:0.14
Consensus pattern (18 bp):
GAAAAAAAATACTAAGAA
Found at i:553520 original size:14 final size:14
Alignment explanation
Indices: 553491--553519 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
553481 TCTGTTTTCC
553491 TTATTTTTTGTGTT
1 TTATTTTTTGTGTT
553505 TTATTTTTTGT-TT
1 TTATTTTTTGTGTT
553518 TT
1 TT
553520 TCTGTATATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.27
14 11 0.73
ACGTcount: A:0.07, C:0.00, G:0.10, T:0.83
Consensus pattern (14 bp):
TTATTTTTTGTGTT
Found at i:558410 original size:11 final size:11
Alignment explanation
Indices: 558394--558428 Score: 70
Period size: 11 Copynumber: 3.2 Consensus size: 11
558384 TTACTTATTT
558394 TTTAAAAGTTG
1 TTTAAAAGTTG
558405 TTTAAAAGTTG
1 TTTAAAAGTTG
558416 TTTAAAAGTTG
1 TTTAAAAGTTG
558427 TT
1 TT
558429 GAGCCTTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.34, C:0.00, G:0.17, T:0.49
Consensus pattern (11 bp):
TTTAAAAGTTG
Found at i:565626 original size:15 final size:15
Alignment explanation
Indices: 565602--565631 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
565592 TATTTGATTT
565602 ATATAATTATTTTAA
1 ATATAATTATTTTAA
*
565617 ATATATTTATTTTAA
1 ATATAATTATTTTAA
565632 TATTTAACAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
ATATAATTATTTTAA
Found at i:567309 original size:2 final size:2
Alignment explanation
Indices: 567304--567328 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
567294 GTTTTTATCA
567304 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
567329 AATGTAGGAT
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:567542 original size:20 final size:20
Alignment explanation
Indices: 567503--567541 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
567493 AACAGACATG
567503 CTTTCATTTTTTCTTTTTTT
1 CTTTCATTTTTTCTTTTTTT
567523 CTTTCATTTTTT-TTTTTTT
1 CTTTCATTTTTTCTTTTTTT
567542 TTTTGGAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.05, C:0.13, G:0.00, T:0.82
Consensus pattern (20 bp):
CTTTCATTTTTTCTTTTTTT
Found at i:574014 original size:26 final size:26
Alignment explanation
Indices: 573984--574055 Score: 83
Period size: 26 Copynumber: 2.8 Consensus size: 26
573974 ATCATAATTG
* *
573984 TCAATTTAACAT-AAAATTAACAAAGT
1 TCAATTTAAAATCAAAAGT-ACAAAGT
* *
574010 TCAATTTAAAATCTAAAGTATAAAGT
1 TCAATTTAAAATCAAAAGTACAAAGT
*
574036 TCAATTTAAAATCTAAAGTA
1 TCAATTTAAAATCAAAAGTA
574056 TAAACAAAGA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
26 37 0.90
27 4 0.10
ACGTcount: A:0.51, C:0.10, G:0.06, T:0.33
Consensus pattern (26 bp):
TCAATTTAAAATCAAAAGTACAAAGT
Found at i:574056 original size:26 final size:26
Alignment explanation
Indices: 574005--574059 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
573995 TAAAATTAAC
574005 AAAGTTCAATTTAAAATCTAAAGTAT
1 AAAGTTCAATTTAAAATCTAAAGTAT
574031 AAAGTTCAATTTAAAATCTAAAGTAT
1 AAAGTTCAATTTAAAATCTAAAGTAT
574057 AAA
1 AAA
574060 CAAAGATTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.53, C:0.07, G:0.07, T:0.33
Consensus pattern (26 bp):
AAAGTTCAATTTAAAATCTAAAGTAT
Found at i:574956 original size:46 final size:49
Alignment explanation
Indices: 574892--575008 Score: 136
Period size: 49 Copynumber: 2.5 Consensus size: 49
574882 TAAATAATGC
** * *
574892 AAATA-AATAAACTCCATGCAAAAT-ATCAT-AATAA-ATCATACAAAT
1 AAATATAATAAAAACCATGCAAAATAATCATCAAAAATATCACACAAAT
574937 AAATATAATAAAAACCATGC-AAATAATCATGCAAAAATATCACACAAAT
1 AAATATAATAAAAACCATGCAAAATAATCAT-CAAAAATATCACACAAAT
* *
574986 AAATATAATAAAAATCATACAAA
1 AAATATAATAAAAACCATGCAAA
575009 TAAATATAAT
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
45 9 0.15
46 17 0.28
48 4 0.07
49 28 0.47
50 2 0.03
ACGTcount: A:0.61, C:0.15, G:0.03, T:0.22
Consensus pattern (49 bp):
AAATATAATAAAAACCATGCAAAATAATCATCAAAAATATCACACAAAT
Found at i:575007 original size:24 final size:24
Alignment explanation
Indices: 574912--575020 Score: 123
Period size: 24 Copynumber: 4.5 Consensus size: 24
574902 ACTCCATGCA
*
574912 AAATATCATAATAAATCATACAAAT
1 AAATATAATAA-AAATCATACAAAT
* *
574937 AAATATAATAAAAACCATGCAAAT
1 AAATATAATAAAAATCATACAAAT
* *
574961 -AATCATGCAA-AAATATCACACAAAT
1 AAAT-AT--AATAAAAATCATACAAAT
574986 AAATATAATAAAAATCATACAAAT
1 AAATATAATAAAAATCATACAAAT
575010 AAATATAATAA
1 AAATATAATAA
575021 TAAAAATCCT
Statistics
Matches: 70, Mismatches: 9, Indels: 11
0.78 0.10 0.12
Matches are distributed among these distances:
23 5 0.07
24 37 0.53
25 23 0.33
26 5 0.07
ACGTcount: A:0.62, C:0.12, G:0.02, T:0.24
Consensus pattern (24 bp):
AAATATAATAAAAATCATACAAAT
Found at i:575024 original size:12 final size:12
Alignment explanation
Indices: 574983--575024 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
574973 ATATCACACA
574983 AATAAATATAAT
1 AATAAATATAAT
574995 AA-AAATCATACA-
1 AATAAAT-ATA-AT
575007 AATAAATATAAT
1 AATAAATATAAT
575019 AATAAA
1 AATAAA
575025 AATCCTACCA
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
11 5 0.19
12 16 0.62
13 5 0.19
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (12 bp):
AATAAATATAAT
Found at i:575127 original size:7 final size:7
Alignment explanation
Indices: 575117--575191 Score: 71
Period size: 7 Copynumber: 10.6 Consensus size: 7
575107 AAAAAGCATG
575117 AAAAAT-
1 AAAAATA
*
575123 AAAAACA
1 AAAAATA
575130 AAAAATA
1 AAAAATA
* *
575137 AGAAATC
1 AAAAATA
*
575144 AAAAATC
1 AAAAATA
*
575151 AAAAATC
1 AAAAATA
*
575158 AAAAATC
1 AAAAATA
575165 AAAAATAA
1 AAAAAT-A
575173 ATAAAATA
1 A-AAAATA
575181 AAAAATA
1 AAAAATA
575188 AAAA
1 AAAA
575192 GAAAAAAAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
6 5 0.08
7 47 0.78
8 3 0.05
9 5 0.08
ACGTcount: A:0.79, C:0.07, G:0.01, T:0.13
Consensus pattern (7 bp):
AAAAATA
Found at i:575184 original size:16 final size:15
Alignment explanation
Indices: 575117--575202 Score: 63
Period size: 14 Copynumber: 5.9 Consensus size: 15
575107 AAAAAGCATG
*
575117 AAAAAT-AAAAA-CA
1 AAAAATAAAAAATAA
* *
575130 AAAAATAAGAAAT-C
1 AAAAATAAAAAATAA
* *
575144 AAAAATCAAAAAT-C
1 AAAAATAAAAAATAA
*
575158 AAAAATCAAAAATAA
1 AAAAATAAAAAATAA
575173 ATAAAATAAAAAATAA
1 A-AAAATAAAAAATAA
*
575189 AAAGAAAAAAAAAT
1 AAA-AATAAAAAAT
575203 CTGTGATCGG
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
13 6 0.10
14 29 0.48
15 3 0.05
16 23 0.38
ACGTcount: A:0.79, C:0.06, G:0.02, T:0.13
Consensus pattern (15 bp):
AAAAATAAAAAATAA
Found at i:575201 original size:23 final size:23
Alignment explanation
Indices: 575123--575202 Score: 67
Period size: 23 Copynumber: 3.6 Consensus size: 23
575113 CATGAAAAAT
* *
575123 AAAAACAAAAAATAAGAAATC--
1 AAAAAAAAAAAATAAAAAATCAA
** *
575144 AAAAATCAAAAATCAAAAATCAA
1 AAAAAAAAAAAATAAAAAATCAA
* *
575167 AAATAAATAAAATAAAAAAT-AA
1 AAAAAAAAAAAATAAAAAATCAA
575189 AAAGAAAAAAAAAT
1 AAA-AAAAAAAAAT
575203 CTGTGATCGG
Statistics
Matches: 45, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
21 17 0.38
22 5 0.11
23 23 0.51
ACGTcount: A:0.79, C:0.06, G:0.03, T:0.12
Consensus pattern (23 bp):
AAAAAAAAAAAATAAAAAATCAA
Found at i:575617 original size:20 final size:20
Alignment explanation
Indices: 575594--575634 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
575584 AAATTTCAAA
* *
575594 TTTAAATAAAATCACAATCT
1 TTTAAAAAAAATCAAAATCT
575614 TTTAAAAAAAATCAAAATCT
1 TTTAAAAAAAATCAAAATCT
575634 T
1 T
575635 ATTTTTACCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.34
Consensus pattern (20 bp):
TTTAAAAAAAATCAAAATCT
Found at i:575960 original size:45 final size:46
Alignment explanation
Indices: 575910--576018 Score: 138
Period size: 44 Copynumber: 2.4 Consensus size: 46
575900 TAGGACTCTG
575910 AAAATTTTAAAAAGCTCTCTC-TT-AAGAG-ATGCTTTGAAATTTTGA
1 AAAATTTTAAAAAGCTCT-TCATTCAAGAGAAT-CTTTGAAATTTTGA
* *
575955 AAAA-TTTAAAAGGCT-TTCATTCAATAGAATCTTTGAAATTTTGA
1 AAAATTTTAAAAAGCTCTTCATTCAAGAGAATCTTTGAAATTTTGA
*
575999 AAAATTTTAAAATGCTCTTC
1 AAAATTTTAAAAAGCTCTTC
576019 TCACCAAAAG
Statistics
Matches: 56, Mismatches: 3, Indels: 9
0.82 0.04 0.13
Matches are distributed among these distances:
42 2 0.04
43 3 0.05
44 32 0.57
45 16 0.29
46 3 0.05
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (46 bp):
AAAATTTTAAAAAGCTCTTCATTCAAGAGAATCTTTGAAATTTTGA
Found at i:576263 original size:42 final size:40
Alignment explanation
Indices: 576120--576338 Score: 136
Period size: 41 Copynumber: 5.2 Consensus size: 40
576110 AGAAGGTTTG
* * * *
576120 AAAATTAAAGAGCT-TATCTCACCAAAGGCTATGAAATTTTT
1 AAAATTAAAGAGCTCT-TCTCACCAAA-GTTGTGAAACTTTA
* * * *
576161 TAAATTAAAGAG-TTTCTCTCACCAGAGGTTATGAAACTTTA
1 AAAATTAAAGAGCTCT-TCTCACCA-AAGTTGTGAAACTTTA
* * *
576202 GAAATTAAAAAGCTATTCTCACCGAAAGTTGTGAAACTTTAA
1 AAAATTAAAGAGCTCTTCTCACC-AAAGTTGTGAAACTTT-A
* * * *
576244 AAAATTAAAGAGCTCTTCTCATCGAAGGTTGTGAAAATTAAAAAA
1 AAAATTAAAGAGCTCTTCTCA-CCAAAGTTGTGAAACTT----TA
* * ** *
576289 AAAATTAAAGAGTTCTTCTCACAAAAAACTGTGAAACTCTA
1 AAAATTAAAGAGCTCTTCTCAC-CAAAGTTGTGAAACTTTA
576330 AAAATTAAA
1 AAAATTAAA
576339 AAGTACTCGA
Statistics
Matches: 141, Mismatches: 26, Indels: 22
0.75 0.14 0.12
Matches are distributed among these distances:
40 1 0.01
41 71 0.50
42 36 0.26
43 1 0.01
44 1 0.01
45 31 0.22
ACGTcount: A:0.44, C:0.14, G:0.13, T:0.29
Consensus pattern (40 bp):
AAAATTAAAGAGCTCTTCTCACCAAAGTTGTGAAACTTTA
Found at i:576322 original size:45 final size:46
Alignment explanation
Indices: 576242--576333 Score: 107
Period size: 45 Copynumber: 2.0 Consensus size: 46
576232 GTGAAACTTT
* ***
576242 AAAAAATTAAAGAGCTCTTCTCATCGAAGGTTGTGAAAAT-TAAAA
1 AAAAAATTAAAGAGCTCTTCTCATCAAAAACTGTGAAAATCTAAAA
* *
576287 AAAAAATTAAAGAGTTCTTCTCA-CAAAAAACTGTGAAACTCTAAAA
1 AAAAAATTAAAGAGCTCTTCTCATC-AAAAACTGTGAAAATCTAAAA
576333 A
1 A
576334 TTAAAAAGTA
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
44 1 0.03
45 32 0.82
46 6 0.15
ACGTcount: A:0.50, C:0.13, G:0.12, T:0.25
Consensus pattern (46 bp):
AAAAAATTAAAGAGCTCTTCTCATCAAAAACTGTGAAAATCTAAAA
Found at i:577505 original size:26 final size:24
Alignment explanation
Indices: 577455--577511 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 24
577445 TTTAAGTCTT
577455 TTTTTTTCACATATTTTTTCATTTA
1 TTTTTTTCACATATTTTTT-ATTTA
577480 TTTTTTTCAACATCTATTTTTT-TTTA
1 TTTTTTTC-ACA--TATTTTTTATTTA
*
577506 TCTTTT
1 TTTTTT
577512 CATTTTCTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
25 8 0.29
26 12 0.43
28 8 0.29
ACGTcount: A:0.18, C:0.12, G:0.00, T:0.70
Consensus pattern (24 bp):
TTTTTTTCACATATTTTTTATTTA
Found at i:581050 original size:22 final size:22
Alignment explanation
Indices: 581022--581067 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
581012 TGATCTTTAG
*
581022 GGTTTTACATGCTAGGTTCAAA
1 GGTTTTACATGCTAAGTTCAAA
581044 GGTTTTACATGCTAAGTTCAAA
1 GGTTTTACATGCTAAGTTCAAA
581066 GG
1 GG
581068 CTCATAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.28, C:0.13, G:0.24, T:0.35
Consensus pattern (22 bp):
GGTTTTACATGCTAAGTTCAAA
Found at i:581354 original size:24 final size:26
Alignment explanation
Indices: 581321--581375 Score: 71
Period size: 24 Copynumber: 2.2 Consensus size: 26
581311 TACAATATTG
581321 TCATACAAAAATA-CTAT-CAA-AATA
1 TCATACAAAAATATC-ATGCAATAATA
*
581345 TCATAGAAAAATATCATGCAATAATA
1 TCATACAAAAATATCATGCAATAATA
581371 TCATA
1 TCATA
581376 ATTAAAACAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
24 14 0.52
25 4 0.15
26 9 0.33
ACGTcount: A:0.55, C:0.15, G:0.04, T:0.27
Consensus pattern (26 bp):
TCATACAAAAATATCATGCAATAATA
Found at i:581357 original size:13 final size:14
Alignment explanation
Indices: 581339--581375 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
581329 AAATACTATC
581339 AAAATATCATAG-A
1 AAAATATCATAGCA
581352 AAAATATCAT-GCA
1 AAAATATCATAGCA
*
581365 ATAATATCATA
1 AAAATATCATA
581376 ATTAAAACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
12 1 0.05
13 20 0.95
ACGTcount: A:0.57, C:0.11, G:0.05, T:0.27
Consensus pattern (14 bp):
AAAATATCATAGCA
Found at i:581485 original size:24 final size:24
Alignment explanation
Indices: 581456--581552 Score: 90
Period size: 24 Copynumber: 4.0 Consensus size: 24
581446 AAGTCACAAT
*
581456 AAATCATGAAAATAGATATAATAA
1 AAATCATGAAAATAAATATAATAA
* * *
581480 AAATCATGCAAGTAATTATGCAA-AA
1 AAATCATGAAAATAAATAT--AATAA
* *
581505 ATATCATGCAAATAAATATAATAA
1 AAATCATGAAAATAAATATAATAA
*
581529 AAATCA-CACAAATAAATATAATAA
1 AAATCATGA-AAATAAATATAATAA
581553 TAAAAATCTT
Statistics
Matches: 59, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
23 2 0.03
24 37 0.63
25 18 0.31
26 2 0.03
ACGTcount: A:0.60, C:0.09, G:0.06, T:0.25
Consensus pattern (24 bp):
AAATCATGAAAATAAATATAATAA
Found at i:581646 original size:22 final size:20
Alignment explanation
Indices: 581612--581692 Score: 76
Period size: 22 Copynumber: 3.9 Consensus size: 20
581602 AATCACAATT
*
581612 AAAAATAATAATAAAACGAAA
1 AAAAATAAAAATAAAAC-AAA
581633 AAAAATTAAAAATAAAAC--A
1 AAAAA-TAAAAATAAAACAAA
*
581652 AAAAATAAGAAATAAAAAAAA
1 AAAAATAA-AAATAAAACAAA
581673 TAAAAATGAAAAAATAAAAC
1 -AAAAAT--AAAAATAAAAC
581693 CTACGATTGG
Statistics
Matches: 50, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
18 3 0.06
19 14 0.28
21 6 0.12
22 17 0.34
23 8 0.16
24 2 0.04
ACGTcount: A:0.79, C:0.04, G:0.04, T:0.14
Consensus pattern (20 bp):
AAAAATAAAAATAAAACAAA
Found at i:581654 original size:19 final size:18
Alignment explanation
Indices: 581630--581672 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
581620 TAATAAAACG
*
581630 AAAAAAAATTAA-AAATA
1 AAAAAAAAATAAGAAATA
581647 AAACAAAAAATAAGAAATA
1 AAA-AAAAAATAAGAAATA
581666 AAAAAAA
1 AAAAAAA
581673 TAAAAATGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 3 0.13
18 12 0.52
19 8 0.35
ACGTcount: A:0.84, C:0.02, G:0.02, T:0.12
Consensus pattern (18 bp):
AAAAAAAAATAAGAAATA
Found at i:581668 original size:14 final size:14
Alignment explanation
Indices: 581612--581691 Score: 60
Period size: 14 Copynumber: 5.7 Consensus size: 14
581602 AATCACAATT
*
581612 AAAAATAATAATAA
1 AAAAATAAAAATAA
*
581626 AACGAAA-AAAAAT-T
1 AA--AAATAAAAATAA
*
581640 AAAAAT-AAAA-CA
1 AAAAATAAAAATAA
581652 AAAAATAAGAAATAAA
1 AAAAATAA-AAAT-AA
*
581668 AAAAATAAAAATGA
1 AAAAATAAAAATAA
581682 AAAAATAAAA
1 AAAAATAAAA
581692 CCTACGATTG
Statistics
Matches: 53, Mismatches: 5, Indels: 16
0.72 0.07 0.22
Matches are distributed among these distances:
12 13 0.25
13 1 0.02
14 18 0.34
15 9 0.17
16 12 0.23
ACGTcount: A:0.80, C:0.03, G:0.04, T:0.14
Consensus pattern (14 bp):
AAAAATAAAAATAA
Found at i:581672 original size:23 final size:24
Alignment explanation
Indices: 581632--581691 Score: 61
Period size: 23 Copynumber: 2.5 Consensus size: 24
581622 ATAAAACGAA
581632 AAAAAATTAAAAATAAAACAAAAAAT-
1 AAAAAA-T-AAAATAAAA-AAAAAATG
* *
581658 AAGAAATAAAA-AAAATAAAAATG
1 AAAAAATAAAATAAAAAAAAAATG
581681 AAAAAATAAAA
1 AAAAAATAAAA
581692 CCTACGATTG
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
22 6 0.20
23 14 0.47
24 4 0.13
25 1 0.03
26 5 0.17
ACGTcount: A:0.82, C:0.02, G:0.03, T:0.13
Consensus pattern (24 bp):
AAAAAATAAAATAAAAAAAAAATG
Found at i:581685 original size:8 final size:7
Alignment explanation
Indices: 581632--581691 Score: 52
Period size: 7 Copynumber: 8.6 Consensus size: 7
581622 ATAAAACGAA
581632 AAAAAAT
1 AAAAAAT
*
581639 TAAAAAT
1 AAAAAAT
*
581646 --AAAAC
1 AAAAAAT
581651 AAAAAAT
1 AAAAAAT
*
581658 AAGAAAT
1 AAAAAAT
*
581665 AAAAAAA
1 AAAAAAT
581672 ATAAAAAT
1 A-AAAAAT
581680 GAAAAAAT
1 -AAAAAAT
581688 AAAA
1 AAAA
581692 CCTACGATTG
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
5 4 0.10
7 26 0.62
8 11 0.26
9 1 0.02
ACGTcount: A:0.82, C:0.02, G:0.03, T:0.13
Consensus pattern (7 bp):
AAAAAAT
Found at i:582568 original size:18 final size:19
Alignment explanation
Indices: 582553--582591 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
582543 ATTGTATTAG
582553 AAACATTGTGTTTATTATTA
1 AAACATTGTGTTTATTA-TA
582573 AAACATTGTGTTTA-TATA
1 AAACATTGTGTTTATTATA
582591 A
1 A
582592 CAAAAACATC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 3 0.16
19 2 0.11
20 14 0.74
ACGTcount: A:0.38, C:0.05, G:0.10, T:0.46
Consensus pattern (19 bp):
AAACATTGTGTTTATTATA
Found at i:582578 original size:20 final size:21
Alignment explanation
Indices: 582547--582587 Score: 75
Period size: 20 Copynumber: 2.0 Consensus size: 21
582537 GCATTTATTG
582547 TATTAGAAACATTGTGTTTAT
1 TATTAGAAACATTGTGTTTAT
582568 TATTA-AAACATTGTGTTTAT
1 TATTAGAAACATTGTGTTTAT
582588 ATAACAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.34, C:0.05, G:0.12, T:0.49
Consensus pattern (21 bp):
TATTAGAAACATTGTGTTTAT
Found at i:582600 original size:22 final size:20
Alignment explanation
Indices: 582553--582600 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 20
582543 ATTGTATTAG
**
582553 AAACATTGTGTTTATTATTA
1 AAACATTGTGTTTATTACAA
582573 AAACATTGTGTTTATATAACAA
1 AAACATTGTGTTTAT-T-ACAA
582595 AAACAT
1 AAACAT
582601 CGTGGTTGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 15 0.62
21 1 0.04
22 8 0.33
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (20 bp):
AAACATTGTGTTTATTACAA
Found at i:583695 original size:15 final size:15
Alignment explanation
Indices: 583675--583717 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
583665 AAATTTTTAT
583675 TTATATATATATGAA
1 TTATATATATATGAA
* *
583690 TTATATATAAATTAA
1 TTATATATATATGAA
*
583705 TTCACATATATAT
1 TT-ATATATATAT
583718 AATAATTAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
15 15 0.65
16 8 0.35
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.47
Consensus pattern (15 bp):
TTATATATATATGAA
Found at i:583751 original size:11 final size:11
Alignment explanation
Indices: 583735--583760 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
583725 AATAAAATAT
583735 ATTTAATTTTA
1 ATTTAATTTTA
583746 ATTTAATTTTA
1 ATTTAATTTTA
583757 ATTT
1 ATTT
583761 TTTATATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
ATTTAATTTTA
Found at i:584976 original size:2 final size:2
Alignment explanation
Indices: 584969--584998 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
584959 GTCTTTATTT
584969 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
584999 AGAATCATAG
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):
TA
Found at i:587751 original size:19 final size:20
Alignment explanation
Indices: 587716--587753 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
587706 TTTTCTTTTA
*
587716 TATAATAAAGCAAAAAAATG
1 TATAAAAAAGCAAAAAAATG
587736 TATAAAAAAG-AAAAAAAT
1 TATAAAAAAGCAAAAAAAT
587754 AAATAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.71, C:0.03, G:0.08, T:0.18
Consensus pattern (20 bp):
TATAAAAAAGCAAAAAAATG
Found at i:587759 original size:19 final size:20
Alignment explanation
Indices: 587717--587760 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
587707 TTTCTTTTAT
* **
587717 ATAATAAAGCAAAAAAATGT
1 ATAAAAAAGCAAAAAAATAA
587737 ATAAAAAAG-AAAAAAATAA
1 ATAAAAAAGCAAAAAAATAA
587756 ATAAA
1 ATAAA
587761 TATTTCTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.75, C:0.02, G:0.07, T:0.16
Consensus pattern (20 bp):
ATAAAAAAGCAAAAAAATAA
Found at i:587817 original size:5 final size:5
Alignment explanation
Indices: 587793--587833 Score: 50
Period size: 5 Copynumber: 8.2 Consensus size: 5
587783 TAATTTATCA
587793 AAAAT -AAAT -AAAT GAAAAT AAAAT AAAAT AAAAT ATAAAT A
1 AAAAT AAAAT AAAAT -AAAAT AAAAT AAAAT AAAAT A-AAAT A
587834 CGCAAATAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
4 8 0.24
5 16 0.48
6 9 0.27
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (5 bp):
AAAAT
Found at i:596064 original size:15 final size:17
Alignment explanation
Indices: 596033--596067 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 17
596023 AGCATCTTTG
596033 TTTTAAATTGAAAAATA
1 TTTTAAATTGAAAAATA
596050 TTTT-AATTG-AAAATA
1 TTTTAAATTGAAAAATA
596065 TTT
1 TTT
596068 ATAGAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 9 0.50
16 5 0.28
17 4 0.22
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.49
Consensus pattern (17 bp):
TTTTAAATTGAAAAATA
Found at i:596945 original size:19 final size:19
Alignment explanation
Indices: 596921--596958 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
596911 TGGGTATCTA
596921 ATGCTAGAAATTGATGCTT
1 ATGCTAGAAATTGATGCTT
596940 ATGCTAGAAATTGATGCTT
1 ATGCTAGAAATTGATGCTT
596959 CTAATAAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.21, T:0.37
Consensus pattern (19 bp):
ATGCTAGAAATTGATGCTT
Found at i:597399 original size:17 final size:17
Alignment explanation
Indices: 597361--597401 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
597351 ACCATTGCTT
597361 TTCTT-GATCTTATCTC
1 TTCTTGGATCTTATCTC
597377 TT-TTGGATCTTTATC-C
1 TTCTTGGATC-TTATCTC
597393 TTCTTGGAT
1 TTCTTGGAT
597402 ATTCTCCAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 2 0.09
16 9 0.41
17 11 0.50
ACGTcount: A:0.12, C:0.20, G:0.12, T:0.56
Consensus pattern (17 bp):
TTCTTGGATCTTATCTC
Found at i:602354 original size:20 final size:20
Alignment explanation
Indices: 602304--602359 Score: 51
Period size: 20 Copynumber: 2.8 Consensus size: 20
602294 AATATTTCAA
* *
602304 ATATATTATTTAATTATGTT
1 ATATTTTATTTAATTATGAT
*
602324 ATATTTAATTTAATTACT-AT
1 ATATTTTATTTAATTA-TGAT
* *
602344 ATTTTTTATTTCATTA
1 ATATTTTATTTAATTA
602360 ATTTCTTGTT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
20 28 0.97
21 1 0.03
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.61
Consensus pattern (20 bp):
ATATTTTATTTAATTATGAT
Found at i:602728 original size:128 final size:128
Alignment explanation
Indices: 602588--602839 Score: 441
Period size: 128 Copynumber: 2.0 Consensus size: 128
602578 TTTATTTTTG
* * *
602588 TTTTTATTTAATAAAATATTTTTATCTGACTTTAGTTAGTGTCGATTTATCTGCATTTAATTGAT
1 TTTTTATTTAATAAAATATTTTTATCTCACTTTAGTTAGTGTCAATTTATCTACATTTAATTGAT
*
602653 ATAAATACTAATTTATTAAGTTAAAGTTTGAGTTTTAAATCGAAATTTAAAATTTATCACATT
66 ATAAATACTAATTTATTAAGTCAAAGTTTGAGTTTTAAATCGAAATTTAAAATTTATCACATT
* *
602716 TTTTTATTTAATAAAATATTTTTATCTCACTTTAGTTAGTGTTAATTTATTTACATTTAATTGAT
1 TTTTTATTTAATAAAATATTTTTATCTCACTTTAGTTAGTGTCAATTTATCTACATTTAATTGAT
*
602781 ATAAATACTCATTTATTAAGTCAAAGTTTGAGTTTTAAATCGAAATTTAAAATTTATCA
66 ATAAATACTAATTTATTAAGTCAAAGTTTGAGTTTTAAATCGAAATTTAAAATTTATCA
602840 TAAAGAATAT
Statistics
Matches: 117, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
128 117 1.00
ACGTcount: A:0.36, C:0.07, G:0.08, T:0.49
Consensus pattern (128 bp):
TTTTTATTTAATAAAATATTTTTATCTCACTTTAGTTAGTGTCAATTTATCTACATTTAATTGAT
ATAAATACTAATTTATTAAGTCAAAGTTTGAGTTTTAAATCGAAATTTAAAATTTATCACATT
Found at i:602881 original size:128 final size:126
Alignment explanation
Indices: 602620--602882 Score: 305
Period size: 128 Copynumber: 2.1 Consensus size: 126
602610 TATCTGACTT
* * *
602620 TAGTTAGTGTCGATTTATCTGCATTTAATTGATATAAATACTAATTTATTAAGTTAAAGTTTGAG
1 TAGTTAGTGTCAATTTATCTACATTTAATTGATATAAATACTAATTTATTAAGTCAAAGTTTGAG
* *** * * ** **
602685 TTTTAAATCGAAATTTAAAATTTATCACATTTTTTTATTTAATAAAATATTTTTATCTCAC
66 TTTTAAATCGAAATTTAAAATTTATCAAAGAATATTATTTAAAAAAATATTAATAAATCAC
* * *
602746 TTTAGTTAGTGTTAATTTATTTACATTTAATTGATATAAATACTCATTTATTAAGTCAAAGTTTG
1 --TAGTTAGTGTCAATTTATCTACATTTAATTGATATAAATACTAATTTATTAAGTCAAAGTTTG
*
602811 AGTTTTAAATCGAAATTTAAAATTTATCATAAAGAATATTA-TTAAAAAAATAAATTAATAAATG
64 AGTTTTAAATCGAAATTTAAAATTTATC--AAAGAATATTATTTAAAAAAAT--ATTAATAAATC
602875 AC
125 AC
602877 -AGTTAG
1 TAGTTAG
602883 CTAATAAAAA
Statistics
Matches: 114, Mismatches: 17, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
128 91 0.80
129 9 0.08
130 6 0.05
131 8 0.07
ACGTcount: A:0.40, C:0.06, G:0.09, T:0.44
Consensus pattern (126 bp):
TAGTTAGTGTCAATTTATCTACATTTAATTGATATAAATACTAATTTATTAAGTCAAAGTTTGAG
TTTTAAATCGAAATTTAAAATTTATCAAAGAATATTATTTAAAAAAATATTAATAAATCAC
Found at i:604262 original size:14 final size:15
Alignment explanation
Indices: 604237--604265 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
604227 TTAATTTTAT
604237 TTATATTTTAAATAA
1 TTATATTTTAAATAA
604252 TTATA-TTTAAATAA
1 TTATATTTTAAATAA
604266 AAATAATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TTATATTTTAAATAA
Found at i:604276 original size:18 final size:18
Alignment explanation
Indices: 604255--604316 Score: 70
Period size: 19 Copynumber: 3.2 Consensus size: 18
604245 TAAATAATTA
604255 TATTTAAATAAAAATAAT
1 TATTTAAATAAAAATAAT
*
604273 TATTATATGATAAATAATAAT
1 TATT-TA-AATAAA-AATAAT
*
604294 TATTTAAATATAAATAAAT
1 TATTTAAATAAAAAT-AAT
604313 TATT
1 TATT
604317 ATTCATAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
18 7 0.19
19 13 0.35
20 7 0.19
21 10 0.27
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (18 bp):
TATTTAAATAAAAATAAT
Found at i:604293 original size:21 final size:20
Alignment explanation
Indices: 604247--604318 Score: 69
Period size: 20 Copynumber: 3.6 Consensus size: 20
604237 TTATATTTTA
* *
604247 AATAATTATATTTAAATAAA-
1 AATAATTAT-TATATATAAAT
604267 AATAATTATTATATGATAAAT
1 AATAATTATTATAT-ATAAAT
*
604288 AATAATTATTTAAATATAAAT
1 AATAATTA-TTATATATAAAT
604309 -A-AATTATTAT
1 AATAATTATTAT
604319 TCATAAAAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
18 3 0.07
19 8 0.18
20 15 0.33
21 14 0.31
22 5 0.11
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (20 bp):
AATAATTATTATATATAAAT
Found at i:604304 original size:24 final size:20
Alignment explanation
Indices: 604262--604338 Score: 70
Period size: 19 Copynumber: 3.9 Consensus size: 20
604252 TTATATTTAA
604262 ATAAAAATAATTATTATATG
1 ATAAAAATAATTATTATATG
*
604282 ATAAATAATAATTATT-TA-A
1 ATAAA-AATAATTATTATATG
* *
604301 ATATAAATAAATTATTAT-TC
1 ATAAAAAT-AATTATTATATG
* *
604321 ATAAAAATTATGATTATA
1 ATAAAAATAATTATTATA
604339 CAAAAAATTA
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
18 3 0.07
19 18 0.39
20 15 0.33
21 10 0.22
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.42
Consensus pattern (20 bp):
ATAAAAATAATTATTATATG
Found at i:604325 original size:39 final size:38
Alignment explanation
Indices: 604245--604325 Score: 110
Period size: 39 Copynumber: 2.1 Consensus size: 38
604235 ATTTATATTT
* *
604245 TAAATAATTATATTTAAATAAAAATAATTATTATATGA
1 TAAATAATAATATTTAAATAAAAATAATTATTATATCA
*
604283 TAAATAATAATTATTTAAATATAAATAAATTATTAT-TCA
1 TAAATAATAA-TATTTAAATAAAAAT-AATTATTATATCA
604322 TAAA
1 TAAA
604326 AATTATGATT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
38 9 0.24
39 20 0.53
40 9 0.24
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (38 bp):
TAAATAATAATATTTAAATAAAAATAATTATTATATCA
Found at i:604526 original size:14 final size:14
Alignment explanation
Indices: 604507--604541 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
604497 AAAGCTAAAA
604507 TTCTTTTCTATTAT
1 TTCTTTTCTATTAT
*
604521 TTCTTTTCTCTTAT
1 TTCTTTTCTATTAT
*
604535 TTATTTT
1 TTCTTTT
604542 TTCTAACAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.74
Consensus pattern (14 bp):
TTCTTTTCTATTAT
Found at i:609632 original size:20 final size:20
Alignment explanation
Indices: 609607--609649 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
609597 CCATTTATCA
609607 ATCCATTCCTTGATAGATTT
1 ATCCATTCCTTGATAGATTT
609627 ATCCATTCCTTGATAGATTT
1 ATCCATTCCTTGATAGATTT
609647 ATC
1 ATC
609650 GTTCCCTACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.26, C:0.21, G:0.09, T:0.44
Consensus pattern (20 bp):
ATCCATTCCTTGATAGATTT
Found at i:618401 original size:15 final size:17
Alignment explanation
Indices: 618381--618417 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
618371 TCAAATAAAT
618381 TAAAATTA-AA-ACAAA
1 TAAAATTATAATACAAA
*
618396 TAAAATTATAATCCAAA
1 TAAAATTATAATACAAA
618413 TAAAA
1 TAAAA
618418 ATACAACTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 8 0.42
16 2 0.11
17 9 0.47
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (17 bp):
TAAAATTATAATACAAA
Found at i:620067 original size:10 final size:10
Alignment explanation
Indices: 620054--620083 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
620044 ATTAAGTTTT
620054 TATATTTTAA
1 TATATTTTAA
620064 TATATTTTAA
1 TATATTTTAA
620074 T-TATTTTAA
1 TATATTTTAA
620083 T
1 T
620084 TGATAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (10 bp):
TATATTTTAA
Found at i:622427 original size:2 final size:2
Alignment explanation
Indices: 622417--622450 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
622407 TTTTTTTATC
622417 TA TA T- TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
622451 CATTATAGTG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 28 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:626536 original size:29 final size:30
Alignment explanation
Indices: 626475--626537 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 30
626465 AGTTTTTGAG
*
626475 TAATGAAACATTTTATATTTTGCTGCAAAGT
1 TAATGAAACATTGTATA-TTTGCTGCAAAGT
626506 TAATGAAACATTGTATA-TTGCTGCAAAGT
1 TAATGAAACATTGTATATTTGCTGCAAAGT
626535 TAA
1 TAA
626538 CCGTGTAGGA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 15 0.48
31 16 0.52
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (30 bp):
TAATGAAACATTGTATATTTGCTGCAAAGT
Found at i:629345 original size:21 final size:22
Alignment explanation
Indices: 629311--629352 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
629301 AATTTAATGT
*
629311 AAAAACTAATAATAT-GTTAAA
1 AAAAACTAAAAATATCGTTAAA
*
629332 AAAAATTAAAAATATCGTTAA
1 AAAAACTAAAAATATCGTTAA
629353 TAATTCAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.29
Consensus pattern (22 bp):
AAAAACTAAAAATATCGTTAAA
Found at i:632173 original size:43 final size:43
Alignment explanation
Indices: 632122--632310 Score: 162
Period size: 41 Copynumber: 4.6 Consensus size: 43
632112 AATATTAGAA
* **
632122 AATATTTAATATTATTTTATTGGTATTTAATATTATTAAACTT
1 AATATTTAATATTATTTAATTAATATTTAATATTATTAAACTT
* * *
632165 AATATTTAATATGATTAAATTAATATTTAATATTGTT---CTGT
1 AATATTTAATATTATTTAATTAATATTTAATATTATTAAACT-T
* *
632206 AATATTTAATATTATTGAA-TAATAGTTAATATTATTAAA-TT
1 AATATTTAATATTATTTAATTAATATTTAATATTATTAAACTT
** * * * *
632247 AATATTTAATAACATTAAATTAATATTCATTA-TATTAAA-TC
1 AATATTTAATATTATTTAATTAATATTTAATATTATTAAACTT
* *
632288 ATTA-TTAATTTTA-TTAATTAATA
1 AATATTTAATATTATTTAATTAATA
632311 ATTTTGATAA
Statistics
Matches: 119, Mismatches: 22, Indels: 14
0.77 0.14 0.09
Matches are distributed among these distances:
39 9 0.08
40 23 0.19
41 46 0.39
42 10 0.08
43 31 0.26
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.51
Consensus pattern (43 bp):
AATATTTAATATTATTTAATTAATATTTAATATTATTAAACTT
Found at i:632189 original size:21 final size:21
Alignment explanation
Indices: 632122--632310 Score: 174
Period size: 21 Copynumber: 9.2 Consensus size: 21
632112 AATATTAGAA
**
632122 AATATTTAATATTATTTTATT
1 AATATTTAATATTATTAAATT
**
632143 GGTATTTAATATTATTAAACTT
1 AATATTTAATATTATTAAA-TT
*
632165 AATATTTAATATGATTAAATT
1 AATATTTAATATTATTAAATT
* *
632186 AATATTTAATATTGTT--CTGT
1 AATATTTAATATTATTAAAT-T
*
632206 AATATTTAATATTATTGAA-T
1 AATATTTAATATTATTAAATT
*
632226 AATAGTTAATATTATTAAATT
1 AATATTTAATATTATTAAATT
**
632247 AATATTTAATAACATTAAATT
1 AATATTTAATATTATTAAATT
* * *
632268 AATATTCATTA-TATTAAATC
1 AATATTTAATATTATTAAATT
* *
632288 ATTA-TTAATTTTATT-AATT
1 AATATTTAATATTATTAAATT
632307 AATA
1 AATA
632311 ATTTTGATAA
Statistics
Matches: 135, Mismatches: 27, Indels: 14
0.77 0.15 0.08
Matches are distributed among these distances:
19 10 0.07
20 48 0.36
21 59 0.44
22 18 0.13
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.51
Consensus pattern (21 bp):
AATATTTAATATTATTAAATT
Found at i:632285 original size:20 final size:20
Alignment explanation
Indices: 632225--632310 Score: 77
Period size: 20 Copynumber: 4.2 Consensus size: 20
632215 TATTATTGAA
632225 TAATAGTTAA-TATTATTAAAT
1 TAATA-TTAATTA-TATTAAAT
* *
632246 TAATATTTAATAACATTAAAT
1 TAATA-TTAATTATATTAAAT
*
632267 TAATATTCATTATATTAAAT
1 TAATATTAATTATATTAAAT
* * *
632287 CATTATTAATTTTATT-AAT
1 TAATATTAATTATATTAAAT
632306 TAATA
1 TAATA
632311 ATTTTGATAA
Statistics
Matches: 52, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
19 6 0.12
20 24 0.46
21 21 0.40
22 1 0.02
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (20 bp):
TAATATTAATTATATTAAAT
Found at i:633098 original size:2 final size:2
Alignment explanation
Indices: 633091--633123 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
633081 AAATCCTAAA
633091 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 A
633124 GCCCCACCAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:633298 original size:21 final size:22
Alignment explanation
Indices: 633274--633321 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
633264 TCACATCCTT
* *
633274 AAAAGGAACAACAGCACA-AAA
1 AAAAGGAAAAAAAGCACATAAA
* *
633295 AAAAAGAAAAAAAGTACATAAA
1 AAAAGGAAAAAAAGCACATAAA
633317 AAAAG
1 AAAAG
633322 TTAAAATACA
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.73, C:0.10, G:0.12, T:0.04
Consensus pattern (22 bp):
AAAAGGAAAAAAAGCACATAAA
Found at i:634373 original size:18 final size:17
Alignment explanation
Indices: 634350--634393 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
634340 TTTTAATTAA
634350 AAATAAAAACTAAAAAAT
1 AAATAAAAA-TAAAAAAT
*
634368 AAATAAATAATAAAATAT
1 AAATAAA-AATAAAAAAT
*
634386 ATATAAAA
1 AAATAAAA
634394 TAATAAAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 1 0.04
18 20 0.87
19 2 0.09
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (17 bp):
AAATAAAAATAAAAAAT
Found at i:634635 original size:14 final size:13
Alignment explanation
Indices: 634616--634650 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
634606 TTTTTTTCAA
634616 TAAATAAATAATAT
1 TAAATAAATAA-AT
634630 TAAATAAATAAAT
1 TAAATAAATAAAT
*
634643 AAAATAAA
1 TAAATAAA
634651 ATTTTATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 9 0.45
14 11 0.55
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
TAAATAAATAAAT
Found at i:634652 original size:18 final size:18
Alignment explanation
Indices: 634614--634652 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
634604 TATTTTTTTC
* *
634614 AATAAATAAATAATATTA
1 AATAAATAAATAAAATAA
634632 AATAAATAAATAAAATAA
1 AATAAATAAATAAAATAA
634650 AAT
1 AAT
634653 TTTATAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (18 bp):
AATAAATAAATAAAATAA
Found at i:635374 original size:23 final size:23
Alignment explanation
Indices: 635344--635390 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
635334 TTTATAGGTT
635344 CTACCTTCTCAACTTGAAAGACA
1 CTACCTTCTCAACTTGAAAGACA
635367 CTACCTTCTCAACTTGAAAGACA
1 CTACCTTCTCAACTTGAAAGACA
635390 C
1 C
635391 CCATTAAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.34, C:0.32, G:0.09, T:0.26
Consensus pattern (23 bp):
CTACCTTCTCAACTTGAAAGACA
Found at i:637933 original size:21 final size:21
Alignment explanation
Indices: 637907--637948 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
637897 TAAATATAAA
637907 GAGATCTCATTTTTATTATTT
1 GAGATCTCATTTTTATTATTT
637928 GAGATCTCATTTTTATTATTT
1 GAGATCTCATTTTTATTATTT
637949 TATTTTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.10, G:0.10, T:0.57
Consensus pattern (21 bp):
GAGATCTCATTTTTATTATTT
Found at i:637958 original size:12 final size:13
Alignment explanation
Indices: 637938--637972 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
637928 GAGATCTCAT
*
637938 TTTTATTATTTTA
1 TTTTATTATTTAA
637951 TTTT-TTATTTAA
1 TTTTATTATTTAA
637963 TTTTATTATT
1 TTTTATTATT
637973 AGATATTACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTATTATTTAA
Found at i:640595 original size:6 final size:6
Alignment explanation
Indices: 640584--640630 Score: 51
Period size: 6 Copynumber: 7.7 Consensus size: 6
640574 TGGACCTAAC
* *
640584 TTTTAT TTTTAT TTTT-T AATTAAT TTTATAT TTTTAT TTTTAT TTTT
1 TTTTAT TTTTAT TTTTAT -TTTTAT TTT-TAT TTTTAT TTTTAT TTTT
640631 TTATATTTTG
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
5 1 0.03
6 27 0.79
7 6 0.18
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (6 bp):
TTTTAT
Found at i:643991 original size:2 final size:2
Alignment explanation
Indices: 643984--644009 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
643974 TGTACATCTT
643984 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
644010 CCACCCTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:657430 original size:10 final size:10
Alignment explanation
Indices: 657415--657450 Score: 63
Period size: 10 Copynumber: 3.6 Consensus size: 10
657405 AAAACAAATC
*
657415 TTAAAATTAA
1 TTAAAATTTA
657425 TTAAAATTTA
1 TTAAAATTTA
657435 TTAAAATTTA
1 TTAAAATTTA
657445 TTAAAA
1 TTAAAA
657451 AGATAATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (10 bp):
TTAAAATTTA
Found at i:659059 original size:7 final size:7
Alignment explanation
Indices: 659049--659078 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
659039 TTTTTTTAGC
659049 TTTTTTA
1 TTTTTTA
659056 TTTTTTA
1 TTTTTTA
659063 TTTTTTA
1 TTTTTTA
659070 TTTTTTA
1 TTTTTTA
659077 TT
1 TT
659079 AGCAAAAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (7 bp):
TTTTTTA
Found at i:665821 original size:23 final size:25
Alignment explanation
Indices: 665776--665823 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
665766 GAATTTAAAG
* *
665776 AAATATTTTTTTATATTTTTAATTA
1 AAATAATTTTTTATATTTCTAATTA
665801 AAATAATTTTTTA-A-TTCTAATTA
1 AAATAATTTTTTATATTTCTAATTA
665824 TTATCCTTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 8 0.38
24 1 0.05
25 12 0.57
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (25 bp):
AAATAATTTTTTATATTTCTAATTA
Found at i:665980 original size:37 final size:37
Alignment explanation
Indices: 665909--665990 Score: 101
Period size: 37 Copynumber: 2.2 Consensus size: 37
665899 AGCCTGTAAT
* * * **
665909 AATTATATATATAATAATATTAAATAGATGTATTTTA
1 AATTTTATATATAATAAAATTAAATAAAAATATTTTA
*
665946 AATTTTATATATAATAAAATTAAGTAAAAATATTTTA
1 AATTTTATATATAATAAAATTAAATAAAAATATTTTA
*
665983 TATTTTAT
1 AATTTTAT
665991 TTTAATTTTG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.48
Consensus pattern (37 bp):
AATTTTATATATAATAAAATTAAATAAAAATATTTTA
Found at i:666144 original size:72 final size:70
Alignment explanation
Indices: 666063--666272 Score: 242
Period size: 71 Copynumber: 2.9 Consensus size: 70
666053 AAAATTAAAC
** ** *
666063 AAAATAAAATTTTAATATCCATTACATTTTTTATCTTAAAAATGTGATTTTTATTAAAATTTAAG
1 AAAATAAAATTTTAATATTTATTA-ATTTTTTATCTTAAAAACATAATTTTTATTAAAATTTAA-
666128 AATTTTG
64 AATTTTG
* * * * *
666135 AAAATAAAATTTTAACATTTATT-ATGATTTTATATTAAAAACACAATCTTTATTAAAATTTTAA
1 AAAATAAAATTTTAATATTTATTAAT-TTTTTATCTTAAAAACATAATTTTTATTAAAA-TTTAA
666199 AATTTTG
64 AATTTTG
* * * *
666206 AAAATAAAATTTCAATATTTATTATATTTTTTATCTTAAAAACATTATTTTTGTTAAAATTTCAA
1 AAAATAAAATTTTAATATTTATTA-ATTTTTTATCTTAAAAACATAATTTTTATTAAAATTTAAA
666271 AT
65 AT
666273 CTTTATTAAA
Statistics
Matches: 115, Mismatches: 19, Indels: 9
0.80 0.13 0.06
Matches are distributed among these distances:
70 2 0.02
71 60 0.52
72 51 0.44
73 2 0.02
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (70 bp):
AAAATAAAATTTTAATATTTATTAATTTTTTATCTTAAAAACATAATTTTTATTAAAATTTAAAA
TTTTG
Found at i:666527 original size:32 final size:32
Alignment explanation
Indices: 666484--666547 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
666474 TTAAAATAAA
*
666484 TTTTATTTCAAATAATTTAATAT-TATTATAT
1 TTTTATTTCAAATAATTTAATATATATAATAT
666515 TTTTCATTTCAAATAATTTAATATATATAATAT
1 TTTT-ATTTCAAATAATTTAATATATATAATAT
666548 ACATATGTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 4 0.13
32 19 0.63
33 7 0.23
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.55
Consensus pattern (32 bp):
TTTTATTTCAAATAATTTAATATATATAATAT
Found at i:666966 original size:15 final size:16
Alignment explanation
Indices: 666936--666979 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
666926 TTGACTTAAG
*
666936 TAAAATTATAAAAATAT
1 TAAAA-TATTAAAATAT
*
666953 TTAAA-ATTAAAATAT
1 TAAAATATTAAAATAT
666968 TAAAATATTAAA
1 TAAAATATTAAA
666980 CTTGTCATCA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
15 13 0.57
16 6 0.26
17 4 0.17
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
TAAAATATTAAAATAT
Found at i:666971 original size:8 final size:8
Alignment explanation
Indices: 666936--666979 Score: 54
Period size: 8 Copynumber: 5.5 Consensus size: 8
666926 TTGACTTAAG
666936 TAAAATTAT
1 TAAAA-TAT
*
666945 AAAAATAT
1 TAAAATAT
*
666953 TTAAA-AT
1 TAAAATAT
666960 TAAAATAT
1 TAAAATAT
666968 TAAAATAT
1 TAAAATAT
666976 TAAA
1 TAAA
666980 CTTGTCATCA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
7 6 0.20
8 20 0.67
9 4 0.13
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (8 bp):
TAAAATAT
Found at i:673596 original size:15 final size:15
Alignment explanation
Indices: 673560--673597 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
673550 AGTATATAAA
* *
673560 AAAGAAACAAAACTT
1 AAAGAAAAAAAAATT
673575 AAA-AAAAAAAAATT
1 AAAGAAAAAAAAATT
673589 AAAGAAAAA
1 AAAGAAAAA
673598 GGGAAGACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.79, C:0.05, G:0.05, T:0.11
Consensus pattern (15 bp):
AAAGAAAAAAAAATT
Found at i:675162 original size:16 final size:17
Alignment explanation
Indices: 675124--675166 Score: 54
Period size: 16 Copynumber: 2.5 Consensus size: 17
675114 TGATTTTAAT
675124 TTTTGAAATATTAAAATA
1 TTTT-AAATATTAAAATA
675142 TTTTAAAT-TTAAACATA
1 TTTTAAATATTAAA-ATA
675159 -TTTAAATA
1 TTTTAAATA
675167 GTTAGATTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 12 0.52
17 7 0.30
18 4 0.17
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (17 bp):
TTTTAAATATTAAAATA
Found at i:675553 original size:26 final size:26
Alignment explanation
Indices: 675500--675557 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
675490 TGGTCCTTCA
* * *
675500 TTTTTTCTAATTTTTTTTTGCCACAT
1 TTTTTTCTAATGTTTATTTGCAACAT
675526 TTTTTTCTAATGTTTATTT-CAACAAT
1 TTTTTTCTAATGTTTATTTGCAAC-AT
675552 TTTTTT
1 TTTTTT
675558 TTTATAATTG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 3 0.11
26 25 0.89
ACGTcount: A:0.19, C:0.12, G:0.03, T:0.66
Consensus pattern (26 bp):
TTTTTTCTAATGTTTATTTGCAACAT
Found at i:676579 original size:36 final size:36
Alignment explanation
Indices: 676538--676610 Score: 101
Period size: 36 Copynumber: 2.0 Consensus size: 36
676528 TCATCATGTC
* * * *
676538 TGGTTTTATTGTCCTTAGTCTTTTGTATATTAGAAA
1 TGGTTTCAATGTCATTAGTCTTTTGTATATGAGAAA
*
676574 TGGTTTCAATGTCATTAGTCTTTTGTTTATGAGAAA
1 TGGTTTCAATGTCATTAGTCTTTTGTATATGAGAAA
676610 T
1 T
676611 AATTAAGAGA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.23, C:0.08, G:0.18, T:0.51
Consensus pattern (36 bp):
TGGTTTCAATGTCATTAGTCTTTTGTATATGAGAAA
Found at i:677048 original size:11 final size:11
Alignment explanation
Indices: 677032--677065 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
677022 TATTATTATT
*
677032 ATAAACGAATA
1 ATAAACAAATA
*
677043 ATAAACAAACA
1 ATAAACAAATA
677054 ATAAACAAATA
1 ATAAACAAATA
677065 A
1 A
677066 GTTTTAAACG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.71, C:0.12, G:0.03, T:0.15
Consensus pattern (11 bp):
ATAAACAAATA
Found at i:678930 original size:6 final size:6
Alignment explanation
Indices: 678919--678948 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
678909 AAAAGCCCAA
*
678919 AATTTT AATTTT AACTTT AATTTT AATTTT
1 AATTTT AATTTT AATTTT AATTTT AATTTT
678949 TAAGTCAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (6 bp):
AATTTT
Done.