Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
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: 50980411
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 52 of 171
Found at i:21347992 original size:30 final size:31
Alignment explanation
Indices: 21347936--21347996 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
21347926 AAAGTTTTCA
* *
21347936 TTAAATCACTAAACTATTCGAAATTTTTTTT
1 TTAAATCACTAAACTATCCCAAATTTTTTTT
*
21347967 TTAAATCACTGAACTA-CCCAAATTTTTTTT
1 TTAAATCACTAAACTATCCCAAATTTTTTTT
21347997 AAGTCACTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 12 0.44
31 15 0.56
ACGTcount: A:0.34, C:0.16, G:0.03, T:0.46
Consensus pattern (31 bp):
TTAAATCACTAAACTATCCCAAATTTTTTTT
Found at i:21349464 original size:13 final size:14
Alignment explanation
Indices: 21349440--21349469 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
21349430 GAACGATCAC
21349440 AAAATAATAAAATA
1 AAAATAATAAAATA
21349454 AAAATAA-AAAATA
1 AAAATAATAAAATA
21349467 AAA
1 AAA
21349470 CATACAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (14 bp):
AAAATAATAAAATA
Found at i:21351579 original size:11 final size:11
Alignment explanation
Indices: 21351563--21351591 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
21351553 CTCTCCCTTT
21351563 CCCTCCCCCTC
1 CCCTCCCCCTC
21351574 CCCTCCCCCTC
1 CCCTCCCCCTC
21351585 CCC-CCCC
1 CCCTCCCC
21351592 TCCTCTCTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.22
11 14 0.78
ACGTcount: A:0.00, C:0.86, G:0.00, T:0.14
Consensus pattern (11 bp):
CCCTCCCCCTC
Found at i:21372489 original size:46 final size:46
Alignment explanation
Indices: 21372438--21372528 Score: 119
Period size: 46 Copynumber: 2.0 Consensus size: 46
21372428 TCACTTTTTT
* * *
21372438 ATTTTTTTTTAACAAATTATATTCAAAGCAATCTTTAAGTATGTTC
1 ATTTTTTTTCAACAAACTATATTCAAAGAAATCTTTAAGTATGTTC
** * *
21372484 ATTTTTTTTCCGCAAACTATATTCAGAGAAATCTTTAAGTGTGTT
1 ATTTTTTTTCAACAAACTATATTCAAAGAAATCTTTAAGTATGTT
21372529 TTAGAGAAGA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
46 38 1.00
ACGTcount: A:0.32, C:0.12, G:0.10, T:0.46
Consensus pattern (46 bp):
ATTTTTTTTCAACAAACTATATTCAAAGAAATCTTTAAGTATGTTC
Found at i:21378168 original size:6 final size:6
Alignment explanation
Indices: 21378159--21378191 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
21378149 TTTTCTTTTT
21378159 TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA TTT
1 TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA TTT
21378192 TGGAATTGCG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.30, C:0.15, G:0.00, T:0.55
Consensus pattern (6 bp):
TTTCAA
Found at i:21379413 original size:19 final size:17
Alignment explanation
Indices: 21379370--21379425 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 17
21379360 TTATCACTAT
21379370 TTTTACAAATTAAATAAA
1 TTTTA-AAATTAAATAAA
21379388 TTATTAAAATTCAAATAAA
1 TT-TTAAAATT-AAATAAA
21379407 TATTTAATAATATAAATAA
1 T-TTTAA-AAT-TAAATAA
21379426 TGTTATAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
18 7 0.21
19 15 0.45
20 10 0.30
21 1 0.03
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (17 bp):
TTTTAAAATTAAATAAA
Found at i:21383171 original size:15 final size:16
Alignment explanation
Indices: 21383142--21383190 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
21383132 CAGTGAAAAT
* *
21383142 ATTTTTAAATATTTTC
1 ATTTTAAAATATTTTA
21383158 ATTTTAAAAT-TTTTA
1 ATTTTAAAATATTTTA
*
21383173 ATTATTAAATTATTTTA
1 ATT-TTAAAATATTTTA
21383190 A
1 A
21383191 ATAAAATAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 7 0.25
16 15 0.54
17 6 0.21
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (16 bp):
ATTTTAAAATATTTTA
Found at i:21390365 original size:55 final size:55
Alignment explanation
Indices: 21390279--21390391 Score: 208
Period size: 55 Copynumber: 2.1 Consensus size: 55
21390269 TTTGAGTAAA
21390279 TTTTGTTTGGAATTCACGTTGTAGTGAAGTGGCTTCTTCCTAATCTCTCAAAGCT
1 TTTTGTTTGGAATTCACGTTGTAGTGAAGTGGCTTCTTCCTAATCTCTCAAAGCT
* *
21390334 TTTTGTTTGGAATTCACGTTGTAGTGGAGTGGCTTCTTCCTAATCTCTCAAGGCT
1 TTTTGTTTGGAATTCACGTTGTAGTGAAGTGGCTTCTTCCTAATCTCTCAAAGCT
21390389 TTT
1 TTT
21390392 ATGTGTCATG
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.18, C:0.18, G:0.21, T:0.43
Consensus pattern (55 bp):
TTTTGTTTGGAATTCACGTTGTAGTGAAGTGGCTTCTTCCTAATCTCTCAAAGCT
Found at i:21395727 original size:45 final size:47
Alignment explanation
Indices: 21395676--21395772 Score: 116
Period size: 42 Copynumber: 2.2 Consensus size: 47
21395666 TGTGAAAAAT
21395676 TAAATAAAAAATTAAAATGACTTT-TTTTTTTTA-AAA-TTGAATGAC
1 TAAATAAAAAATTAAAAT-ACTTTATTTTTTTTATAAAGTTGAATGAC
** *
21395721 TAAAT---AAATTATTATACTTTATTTTTTTTATAAAGTTGAATGGC
1 TAAATAAAAAATTAAAATACTTTATTTTTTTTATAAAGTTGAATGAC
21395765 TAAATAAA
1 TAAATAAA
21395773 TTATTACACT
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
41 5 0.12
42 17 0.40
43 3 0.07
44 13 0.30
45 5 0.12
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.44
Consensus pattern (47 bp):
TAAATAAAAAATTAAAATACTTTATTTTTTTTATAAAGTTGAATGAC
Found at i:21395761 original size:44 final size:42
Alignment explanation
Indices: 21395695--21395791 Score: 151
Period size: 44 Copynumber: 2.3 Consensus size: 42
21395685 AATTAAAATG
*
21395695 ACTTT-TTTTTTTTAAAATTGAATGACTAAATAAATTATTAT
1 ACTTTATTTTTTTTAAAATTGAATGACTAAATAAATTATTAC
*
21395736 ACTTTATTTTTTTTATAAAGTTGAATGGCTAAATAAATTATTAC
1 ACTTTATTTTTTTTA-AAA-TTGAATGACTAAATAAATTATTAC
21395780 ACTTTATTTTTT
1 ACTTTATTTTTT
21395792 CATAAGAAAT
Statistics
Matches: 51, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
41 5 0.10
42 9 0.18
43 3 0.06
44 34 0.67
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.53
Consensus pattern (42 bp):
ACTTTATTTTTTTTAAAATTGAATGACTAAATAAATTATTAC
Found at i:21396708 original size:23 final size:24
Alignment explanation
Indices: 21396678--21396726 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 24
21396668 AACAGTGTAA
*
21396678 ATATGTAATGATAGTT-AAAACTT
1 ATATGTAACGATAGTTAAAAACTT
*
21396701 ATATGTAACGATGGTTAAAAACTT
1 ATATGTAACGATAGTTAAAAACTT
21396725 AT
1 AT
21396727 CAAATTCTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 14 0.61
24 9 0.39
ACGTcount: A:0.43, C:0.06, G:0.14, T:0.37
Consensus pattern (24 bp):
ATATGTAACGATAGTTAAAAACTT
Found at i:21405634 original size:25 final size:25
Alignment explanation
Indices: 21405600--21405658 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 25
21405590 AATATTTATA
21405600 TTATATTATTTTAATAT-TTAATAATT
1 TTATA-TATTTTAATATATTAA-AATT
* *
21405626 TTATATATTTTTATTTATTAAAATT
1 TTATATATTTTAATATATTAAAATT
*
21405651 TTGTATAT
1 TTATATAT
21405659 AGTTATCTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
25 20 0.69
26 9 0.31
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.63
Consensus pattern (25 bp):
TTATATATTTTAATATATTAAAATT
Found at i:21405936 original size:16 final size:15
Alignment explanation
Indices: 21405912--21405955 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 15
21405902 GATCTGGGAA
21405912 AAAATAAAAATAAAAG
1 AAAA-AAAAATAAAAG
*
21405928 AAAACAAAATTAAAAG
1 AAAA-AAAAATAAAAG
21405944 AAATAAAAAATA
1 AAA-AAAAAATA
21405956 GGAGTGTCGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 23 0.96
17 1 0.04
ACGTcount: A:0.80, C:0.02, G:0.05, T:0.14
Consensus pattern (15 bp):
AAAAAAAAATAAAAG
Found at i:21410486 original size:28 final size:28
Alignment explanation
Indices: 21410448--21410507 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 28
21410438 ATCAGTAATG
* *
21410448 TTTAAAGCAACGGATTTTGCTTTTGAGT
1 TTTAAAGCAACAGATTTTACTTTTGAGT
*
21410476 TTTAAAGCAACAGCTTTTACTTTTGAGT
1 TTTAAAGCAACAGATTTTACTTTTGAGT
21410504 TTTA
1 TTTA
21410508 TGAGCAATGT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.27, C:0.12, G:0.17, T:0.45
Consensus pattern (28 bp):
TTTAAAGCAACAGATTTTACTTTTGAGT
Found at i:21415193 original size:33 final size:32
Alignment explanation
Indices: 21415146--21415210 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 32
21415136 AATTTATTCA
21415146 AATAAACATAAC-TTTCAAAAAAGACTTATAATG
1 AATAAACATAACTTTTCAAAAAA-A-TTATAATG
* *
21415179 AATAAACATTACTTTTCTAAAAAATTATAATG
1 AATAAACATAACTTTTCAAAAAAATTATAATG
21415211 TTATAGACGT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 8 0.28
33 12 0.41
34 9 0.31
ACGTcount: A:0.52, C:0.11, G:0.05, T:0.32
Consensus pattern (32 bp):
AATAAACATAACTTTTCAAAAAAATTATAATG
Found at i:21419923 original size:28 final size:29
Alignment explanation
Indices: 21419891--21419949 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
21419881 TATTTAGAGG
*
21419891 GTCCTTAGAGATA-CCCCATACCTATGTT
1 GTCCTTAGAGATATCCCAATACCTATGTT
21419919 GTCCTTAGAGATATCCCAATACCTATGTT
1 GTCCTTAGAGATATCCCAATACCTATGTT
21419948 GT
1 GT
21419950 TAACATGAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 13 0.45
29 16 0.55
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.34
Consensus pattern (29 bp):
GTCCTTAGAGATATCCCAATACCTATGTT
Found at i:21424661 original size:11 final size:11
Alignment explanation
Indices: 21424637--21424689 Score: 56
Period size: 11 Copynumber: 4.8 Consensus size: 11
21424627 GATTTATTGA
*
21424637 ATTTTGATTTT
1 ATTTTTATTTT
21424648 -TTTTT-TTTT
1 ATTTTTATTTT
21424657 ATTTTTATTTT
1 ATTTTTATTTT
*
21424668 ATTTTTATATAT
1 ATTTTTAT-TTT
21424680 ATTTATTATT
1 ATTT-TTATT
21424690 GATCCTTAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
9 4 0.11
10 9 0.25
11 12 0.33
12 7 0.19
13 4 0.11
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (11 bp):
ATTTTTATTTT
Found at i:21424684 original size:21 final size:20
Alignment explanation
Indices: 21424643--21424686 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
21424633 TTGAATTTTG
* * *
21424643 ATTTTTTTTTTTTTATTTTT
1 ATTTTTTTTTATATATATTT
21424663 ATTTTATTTTTATATATATTT
1 ATTTT-TTTTTATATATATTT
21424684 ATT
1 ATT
21424687 ATTGATCCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (20 bp):
ATTTTTTTTTATATATATTT
Found at i:21426167 original size:18 final size:18
Alignment explanation
Indices: 21426144--21426186 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
21426134 GAATAGATGT
21426144 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
* *
21426162 TTAATTGAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
21426180 TTAATTA
1 TTAATTA
21426187 CACATTGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:21428343 original size:23 final size:23
Alignment explanation
Indices: 21428299--21428344 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
21428289 TATATAAAAT
* *
21428299 AAATAAATAATAATATTTTTAAA
1 AAATAAATAATAAAATTATTAAA
21428322 AAAT-AATAATTAAAATTATTAAA
1 AAATAAATAA-TAAAATTATTAAA
21428345 TGTTGAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (23 bp):
AAATAAATAATAAAATTATTAAA
Found at i:21428881 original size:15 final size:15
Alignment explanation
Indices: 21428861--21428891 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
21428851 GTTAGTAACC
21428861 TACAAAATATTATGT
1 TACAAAATATTATGT
21428876 TACAAAATATTATGT
1 TACAAAATATTATGT
21428891 T
1 T
21428892 TGTAACTCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.42
Consensus pattern (15 bp):
TACAAAATATTATGT
Found at i:21431214 original size:2 final size:2
Alignment explanation
Indices: 21431207--21431242 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
21431197 CCCAAGACCA
21431207 AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
21431243 ACCATGTACA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21431232 original size:17 final size:17
Alignment explanation
Indices: 21431210--21431242 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
21431200 AAGACCAATA
21431210 TATATATATATATATAT
1 TATATATATATATATAT
21431227 TATATATATATATATA
1 TATATATATATATATA
21431243 ACCATGTACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TATATATATATATATAT
Found at i:21431852 original size:27 final size:28
Alignment explanation
Indices: 21431822--21431893 Score: 85
Period size: 27 Copynumber: 2.6 Consensus size: 28
21431812 CATATAATAC
21431822 AAAAAAATAAAAATTAT-AACAATATGA
1 AAAAAAATAAAAATTATAAACAATATGA
* * *
21431849 AAAATAATAATAA-TATAAACTATATGA
1 AAAAAAATAAAAATTATAAACAATATGA
*
21431876 AAAAAATAAAAAAATTAT
1 AAAAAA-ATAAAAATTAT
21431894 TAAAATCTCG
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
26 3 0.08
27 25 0.69
28 5 0.14
29 3 0.08
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.25
Consensus pattern (28 bp):
AAAAAAATAAAAATTATAAACAATATGA
Found at i:21431853 original size:18 final size:18
Alignment explanation
Indices: 21431830--21431864 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
21431820 ACAAAAAAAT
*
21431830 AAAAATTATAACAATATG
1 AAAAATAATAACAATATG
*
21431848 AAAAATAATAATAATAT
1 AAAAATAATAACAATAT
21431865 AAACTATATG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.29
Consensus pattern (18 bp):
AAAAATAATAACAATATG
Found at i:21444879 original size:301 final size:300
Alignment explanation
Indices: 21444317--21444915 Score: 1083
Period size: 301 Copynumber: 2.0 Consensus size: 300
21444307 CCTAAGAATA
*
21444317 CTATCTATACTTAGTATTGGACAACGAAGAAAATCAGGGAGATCGGTTTGCAATTATGGGAATAA
1 CTATCTATACTTAGTATTGGACAACGAAGAAAATCAGGGAGATCGATTTGCAATTATGGGAATAA
*
21444382 ATTATAAAGTGCACTGCATTAGATGAAAGAAATCATCTCGTACATGAACAATACCTCTAACTCTA
66 ATTATAAAGTGCACCGCATTAGATGAAAGAAATCATCTCGTACATGAACAATACCTCTAACTCTA
*
21444447 GCTCATTTACAAAGCCCACAACTGCACACCCATCAATTCATTCTCACAACACACACATAAATACA
131 GCTCATTTACAAAGCCCACAACTGCACACCCATCAATTCATTCTCACAACACACACATAAACACA
21444512 AAATAAAAAATAAACAGGAAAAAAAAGCACCTTCTCAATGAAGAACTACATTTCAAGGACTATTC
196 AAATAAAAAATAAACAGGAAAAAAAAGCACCTTCTCAATGAAGAACTACATTTCAA-GACTATTC
*
21444577 ATAATAATTCTTATACAACAAAGAAAATCGGGGAGATCAAT
260 ATAATAATTCTTATACAACAAAGAAAATCAGGGAGATCAAT
21444618 CTATCTATACTTAGTATTGGACAACGAAGAAAATCAGGGAGATCGATTTGCAATTATGGGAATAA
1 CTATCTATACTTAGTATTGGACAACGAAGAAAATCAGGGAGATCGATTTGCAATTATGGGAATAA
*
21444683 ATTATAAGGTGCACCGCATTAGATGAAAGAAATCATCTCGTACATGAACAATACCTCTAACTCTA
66 ATTATAAAGTGCACCGCATTAGATGAAAGAAATCATCTCGTACATGAACAATACCTCTAACTCTA
* *
21444748 GCTCATTTACAAAGCCCACAACTGCACACCCATGAATTCATTCTCACAAACTCACACATAAACAC
131 GCTCATTTACAAAGCCCACAACTGCACACCCATCAATTCATTCTCAC-AACACACACATAAACAC
*
21444813 AAAATAAAAAATAAACAGGAAAAAAAAAGCACCTTCTCAATGAAGAACTACATTTCAA-AGTATT
195 AAAATAAAAAATAAACAGG-AAAAAAAAGCACCTTCTCAATGAAGAACTACATTTCAAGACTATT
*
21444877 CATAATAATTCTTATACAACGAAGAAAATCAGGGAGATC
259 CATAATAATTCTTATACAACAAAGAAAATCAGGGAGATC
21444916 GATTTGCAAT
Statistics
Matches: 287, Mismatches: 9, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
301 215 0.75
302 34 0.12
303 38 0.13
ACGTcount: A:0.43, C:0.20, G:0.13, T:0.24
Consensus pattern (300 bp):
CTATCTATACTTAGTATTGGACAACGAAGAAAATCAGGGAGATCGATTTGCAATTATGGGAATAA
ATTATAAAGTGCACCGCATTAGATGAAAGAAATCATCTCGTACATGAACAATACCTCTAACTCTA
GCTCATTTACAAAGCCCACAACTGCACACCCATCAATTCATTCTCACAACACACACATAAACACA
AAATAAAAAATAAACAGGAAAAAAAAGCACCTTCTCAATGAAGAACTACATTTCAAGACTATTCA
TAATAATTCTTATACAACAAAGAAAATCAGGGAGATCAAT
Found at i:21448303 original size:15 final size:15
Alignment explanation
Indices: 21448283--21448311 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
21448273 CTAATTTTTT
21448283 GGACGATTTCCTCCA
1 GGACGATTTCCTCCA
21448298 GGACGATTTCCTCC
1 GGACGATTTCCTCC
21448312 GCTACTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.34, G:0.21, T:0.28
Consensus pattern (15 bp):
GGACGATTTCCTCCA
Found at i:21450259 original size:2 final size:2
Alignment explanation
Indices: 21450252--21450294 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
21450242 TCTCCCTTCA
21450252 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
21450294 C
1 C
21450295 CCCCATGTAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:21451777 original size:2 final size:2
Alignment explanation
Indices: 21451770--21451803 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
21451760 ACAGGATTTG
21451770 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
21451804 TTATATATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:21460105 original size:21 final size:19
Alignment explanation
Indices: 21460076--21460118 Score: 50
Period size: 21 Copynumber: 2.2 Consensus size: 19
21460066 GCAATTTGGA
21460076 GTAAAGACTTAAAAGTACTAT
1 GTAAAGACTTAAAA-T-CTAT
* *
21460097 GTAATGACTTGAAATCTAT
1 GTAAAGACTTAAAATCTAT
21460116 GTA
1 GTA
21460119 TTTTGTGTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 7 0.35
20 1 0.05
21 12 0.60
ACGTcount: A:0.42, C:0.09, G:0.16, T:0.33
Consensus pattern (19 bp):
GTAAAGACTTAAAATCTAT
Found at i:21461276 original size:23 final size:22
Alignment explanation
Indices: 21461228--21461276 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
21461218 ATCCTTTAAA
*
21461228 TAAATACTTATATTTATATTAT
1 TAAATACTTATATTTATATAAT
*
21461250 TAAATATTTCATATTT-TATAAT
1 TAAATACTT-ATATTTATATAAT
21461272 GTAAA
1 -TAAA
21461277 ATATATTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 13 0.57
23 10 0.43
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (22 bp):
TAAATACTTATATTTATATAAT
Found at i:21461672 original size:37 final size:36
Alignment explanation
Indices: 21461631--21461736 Score: 99
Period size: 37 Copynumber: 3.2 Consensus size: 36
21461621 TTTATATTCC
21461631 ATATGTTATAATATTAACAAATTTGAATATTATTTAA
1 ATATGTTATAATATTAA-AAATTTGAATATTATTTAA
*
21461668 ATATG-TAT--T-TT----TTTTAGAA-A--ATTTAA
1 ATATGTTATAATATTAAAAATTT-GAATATTATTTAA
21461694 ATATGTTATAATATTAATAAATTTGAATATTATTTAA
1 ATATGTTATAATATTAA-AAATTTGAATATTATTTAA
21461731 ATATGT
1 ATATGT
21461737 ATTTTTTTAG
Statistics
Matches: 54, Mismatches: 2, Indels: 26
0.66 0.02 0.32
Matches are distributed among these distances:
26 11 0.20
27 3 0.06
28 4 0.07
29 4 0.07
30 2 0.04
33 2 0.04
34 4 0.07
35 4 0.07
36 3 0.06
37 17 0.31
ACGTcount: A:0.43, C:0.01, G:0.07, T:0.49
Consensus pattern (36 bp):
ATATGTTATAATATTAAAAATTTGAATATTATTTAA
Found at i:21461774 original size:62 final size:63
Alignment explanation
Indices: 21461631--21461759 Score: 242
Period size: 63 Copynumber: 2.1 Consensus size: 63
21461621 TTTATATTCC
*
21461631 ATATGTTATAATATTAACAAATTTGAATATTATTTAAATATGTATTTTTTTTAGAAAATTTAA
1 ATATGTTATAATATTAATAAATTTGAATATTATTTAAATATGTATTTTTTTTAGAAAATTTAA
21461694 ATATGTTATAATATTAATAAATTTGAATATTATTTAAATATGTA-TTTTTTTAGAAAATTTAA
1 ATATGTTATAATATTAATAAATTTGAATATTATTTAAATATGTATTTTTTTTAGAAAATTTAA
21461756 ATAT
1 ATAT
21461760 ATTTATTTTA
Statistics
Matches: 65, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
62 22 0.34
63 43 0.66
ACGTcount: A:0.43, C:0.01, G:0.06, T:0.50
Consensus pattern (63 bp):
ATATGTTATAATATTAATAAATTTGAATATTATTTAAATATGTATTTTTTTTAGAAAATTTAA
Found at i:21465568 original size:7 final size:7
Alignment explanation
Indices: 21465556--21465580 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
21465546 TCCAGATTCA
21465556 TTCCTTC
1 TTCCTTC
21465563 TTCCTTC
1 TTCCTTC
21465570 TTCCTTC
1 TTCCTTC
21465577 TTCC
1 TTCC
21465581 AAGACAAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (7 bp):
TTCCTTC
Found at i:21472137 original size:12 final size:12
Alignment explanation
Indices: 21472128--21472152 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
21472118 TCTTCTCCTC
21472128 TATTTTCTCCCT
1 TATTTTCTCCCT
21472140 TATTTTCTCCCT
1 TATTTTCTCCCT
21472152 T
1 T
21472153 CTCCATCTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.32, G:0.00, T:0.60
Consensus pattern (12 bp):
TATTTTCTCCCT
Found at i:21472747 original size:28 final size:29
Alignment explanation
Indices: 21472716--21472775 Score: 81
Period size: 28 Copynumber: 2.1 Consensus size: 29
21472706 AAGTATAGTG
*
21472716 TTCAATG-TTTAAGGTTTA-AGATTTAGGA
1 TTCAATGATTTAAAGTTTAGAG-TTTAGGA
21472744 TTC-ATGATTTAAAGTTTAGAGTTTAGGA
1 TTCAATGATTTAAAGTTTAGAGTTTAGGA
21472772 TTCA
1 TTCA
21472776 GGGTCAAGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
27 3 0.11
28 23 0.82
29 2 0.07
ACGTcount: A:0.32, C:0.05, G:0.20, T:0.43
Consensus pattern (29 bp):
TTCAATGATTTAAAGTTTAGAGTTTAGGA
Found at i:21475372 original size:43 final size:43
Alignment explanation
Indices: 21475287--21475479 Score: 165
Period size: 43 Copynumber: 4.5 Consensus size: 43
21475277 TGCTATTGAC
* * * * * *
21475287 CGACGTTTTTCCCACAAACGCCACTAAAGATCATGTTCTTTAG
1 CGACGCTTCTCCCACAAACGCCGCGAAAGAACATGATCTTTAG
** * * *
21475330 CGGTGCTTCTCCCACAAACGCTGCGAAATAACATGATTTTTAG
1 CGACGCTTCTCCCACAAACGCCGCGAAAGAACATGATCTTTAG
* * * * * *
21475373 AGACGCTTTTACCACAAACACCGTTG-AAGAACATGGTCTTTAG
1 CGACGCTTCTCCCACAAACGCCG-CGAAAGAACATGATCTTTAG
* *
21475416 CGACGCTTCTCCCACAAACGCCACTAAAGAACATGATCTTTAG
1 CGACGCTTCTCCCACAAACGCCGCGAAAGAACATGATCTTTAG
* *
21475459 CGGCGCCTT-TCACACAAACGC
1 CGACG-CTTCTCCCACAAACGC
21475480 TTTTATACAA
Statistics
Matches: 115, Mismatches: 32, Indels: 6
0.75 0.21 0.04
Matches are distributed among these distances:
43 111 0.97
44 4 0.03
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.25
Consensus pattern (43 bp):
CGACGCTTCTCCCACAAACGCCGCGAAAGAACATGATCTTTAG
Found at i:21475475 original size:86 final size:86
Alignment explanation
Indices: 21475313--21475477 Score: 206
Period size: 86 Copynumber: 1.9 Consensus size: 86
21475303 AACGCCACTA
* * ** ** * *
21475313 AAGATCATGTTCTTTAGCGGTGCTTCTCCCACAAACGCTGCGAAATAACATGATTTTTAGAGACG
1 AAGAACATGGTCTTTAGCGACGCTTCTCCCACAAACGCCACGAAAGAACATGATCTTTAGAGACG
*
21475378 CTTTTACCACAAACACCGTTG
66 CTTTCACCACAAACACCGTTG
* * *
21475399 AAGAACATGGTCTTTAGCGACGCTTCTCCCACAAACGCCACTAAAGAACATGATCTTTAGCGGCG
1 AAGAACATGGTCTTTAGCGACGCTTCTCCCACAAACGCCACGAAAGAACATGATCTTTAGAGACG
21475464 CCTTTCA-CACAAAC
66 -CTTTCACCACAAAC
21475478 GCTTTTATAC
Statistics
Matches: 66, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
86 61 0.92
87 5 0.08
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.25
Consensus pattern (86 bp):
AAGAACATGGTCTTTAGCGACGCTTCTCCCACAAACGCCACGAAAGAACATGATCTTTAGAGACG
CTTTCACCACAAACACCGTTG
Found at i:21485253 original size:1 final size:1
Alignment explanation
Indices: 21485247--21485271 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
21485237 CATTTATATT
21485247 GGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGG
21485272 CAAAAGAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:21488227 original size:21 final size:23
Alignment explanation
Indices: 21488186--21488229 Score: 74
Period size: 21 Copynumber: 2.0 Consensus size: 23
21488176 TAATTGAATT
21488186 TTTTTAATATAAGTGATATTTTA
1 TTTTTAATATAAGTGATATTTTA
21488209 TTTTTAA-ATAAGT-ATATTTTA
1 TTTTTAATATAAGTGATATTTTA
21488230 AATATTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 8 0.38
22 6 0.29
23 7 0.33
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (23 bp):
TTTTTAATATAAGTGATATTTTA
Found at i:21488237 original size:22 final size:22
Alignment explanation
Indices: 21488189--21488238 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 22
21488179 TTGAATTTTT
* *
21488189 TTAATATAAGTGATATTTTATTT
1 TTAA-ATAAGTGATATTTTAATA
21488212 TTAAATAAGT-ATATTTTAAATA
1 TTAAATAAGTGATATTTT-AATA
21488234 TTAAA
1 TTAAA
21488239 ATATAATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 7 0.29
22 13 0.54
23 4 0.17
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (22 bp):
TTAAATAAGTGATATTTTAATA
Found at i:21488244 original size:25 final size:24
Alignment explanation
Indices: 21488216--21488278 Score: 60
Period size: 24 Copynumber: 2.6 Consensus size: 24
21488206 TTATTTTTAA
21488216 ATAAGTATATTTTAAATATTAAAAT
1 ATAAGTATATTTTAAA-ATTAAAAT
*
21488241 ATAA-TA-ATTTTTAAAATTAATAT
1 ATAAGTATA-TTTTAAAATTAAAAT
*
21488264 TTAATGTAT-TTTTAA
1 ATAA-GTATATTTTAA
21488279 TATACTCAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
23 11 0.34
24 15 0.47
25 6 0.19
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (24 bp):
ATAAGTATATTTTAAAATTAAAAT
Found at i:21488268 original size:23 final size:25
Alignment explanation
Indices: 21488225--21488278 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
21488215 AATAAGTATA
21488225 TTTTAAATATTAAAATATAAT-AAT
1 TTTTAAATATTAAAATATAATGAAT
* * *
21488249 TTTTAAA-ATTAATATTTAATGTAT
1 TTTTAAATATTAAAATATAATGAAT
21488273 TTTTAA
1 TTTTAA
21488279 TATACTCAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 11 0.42
24 15 0.58
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (25 bp):
TTTTAAATATTAAAATATAATGAAT
Found at i:21488822 original size:2 final size:2
Alignment explanation
Indices: 21488817--21488841 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
21488807 AAAAAAAAAA
21488817 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
21488842 ATAAAGTGTG
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:21496934 original size:20 final size:22
Alignment explanation
Indices: 21496909--21496960 Score: 72
Period size: 20 Copynumber: 2.5 Consensus size: 22
21496899 ATAAAATAAT
21496909 TATTAATAAATATTTA-TAAAA
1 TATTAATAAATATTTATTAAAA
* *
21496930 T-TTAATATATTTTTATTAAAA
1 TATTAATAAATATTTATTAAAA
21496951 TATTAATAAA
1 TATTAATAAA
21496961 AATATTTTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 12 0.46
21 7 0.27
22 7 0.27
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TATTAATAAATATTTATTAAAA
Found at i:21497093 original size:18 final size:18
Alignment explanation
Indices: 21497054--21497093 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
21497044 TAAAATAATA
*
21497054 AATAATATTAATTATATT
1 AATAATATTAATTATATG
21497072 AATAATATTATATTAT-TG
1 AATAATATTA-ATTATATG
21497090 AATA
1 AATA
21497094 TAAAAATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (18 bp):
AATAATATTAATTATATG
Found at i:21501267 original size:9 final size:9
Alignment explanation
Indices: 21501253--21501341 Score: 67
Period size: 9 Copynumber: 9.8 Consensus size: 9
21501243 ATAAATATCA
21501253 ATAAAAATT
1 ATAAAAATT
*
21501262 ATAAAAATC
1 ATAAAAATT
* *
21501271 ATTAAATTT
1 ATAAAAATT
21501280 AATAAAAA-T
1 -ATAAAAATT
*
21501289 ATAAAAAAT
1 ATAAAAATT
*
21501298 -TAAAATTT
1 ATAAAAATT
21501306 ATTAAAAATAT
1 A-TAAAAAT-T
*
21501317 AAAAAAATT
1 ATAAAAATT
21501326 AT-AAAATAT
1 ATAAAAAT-T
21501335 ATAAAAA
1 ATAAAAA
21501342 AAAGACTTTT
Statistics
Matches: 62, Mismatches: 11, Indels: 13
0.72 0.13 0.15
Matches are distributed among these distances:
8 18 0.29
9 21 0.34
10 21 0.34
11 2 0.03
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.31
Consensus pattern (9 bp):
ATAAAAATT
Found at i:21501271 original size:19 final size:18
Alignment explanation
Indices: 21501243--21501341 Score: 60
Period size: 18 Copynumber: 5.4 Consensus size: 18
21501233 GTGGTAAAAA
*
21501243 ATAAATATCAATAAAAATT
1 ATAAAAATC-ATAAAAATT
* *
21501262 ATAAAAATCATTAAATTT
1 ATAAAAATCATAAAAATT
*
21501280 AATAAAAAT-ATAAAAAAT
1 -ATAAAAATCATAAAAATT
* *
21501298 -TAAAATTTATTAAAAATAT
1 ATAAAAATCA-TAAAAAT-T
* *
21501317 AAAAAAATTAT-AAAATAT
1 ATAAAAATCATAAAAAT-T
21501335 ATAAAAA
1 ATAAAAA
21501342 AAAGACTTTT
Statistics
Matches: 64, Mismatches: 11, Indels: 11
0.74 0.13 0.13
Matches are distributed among these distances:
16 6 0.09
17 1 0.02
18 32 0.50
19 18 0.28
20 7 0.11
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (18 bp):
ATAAAAATCATAAAAATT
Found at i:21501297 original size:20 final size:19
Alignment explanation
Indices: 21501253--21501343 Score: 66
Period size: 20 Copynumber: 4.9 Consensus size: 19
21501243 ATAAATATCA
* *
21501253 ATAAAAAT-TATAAAAATC
1 ATAAAAATATAAAAAAATT
* *
21501271 AT-TAAATTTAATAAAAA-T
1 ATAAAAATATAA-AAAAATT
* *
21501289 ATAAAAA-AT-TAAAATTT
1 ATAAAAATATAAAAAAATT
21501306 ATTAAAAATATAAAAAAATT
1 A-TAAAAATATAAAAAAATT
21501326 ATAAAATATATAAAAAAA
1 ATAAAA-ATATAAAAAAA
21501344 AGACTTTTTA
Statistics
Matches: 56, Mismatches: 9, Indels: 14
0.71 0.11 0.18
Matches are distributed among these distances:
16 4 0.07
17 6 0.11
18 13 0.23
19 15 0.27
20 18 0.32
ACGTcount: A:0.68, C:0.01, G:0.00, T:0.31
Consensus pattern (19 bp):
ATAAAAATATAAAAAAATT
Found at i:21501303 original size:26 final size:25
Alignment explanation
Indices: 21501237--21501322 Score: 102
Period size: 26 Copynumber: 3.3 Consensus size: 25
21501227 ATATATGTGG
*
21501237 TAAAAAA-TAAATATCAATAAAAATTA
1 TAAAAAATTAAAT-TTAATAAAAA-TA
21501263 TAAAAATCATTAAATTTAATAAAAATA
1 TAAAAA--ATTAAATTTAATAAAAATA
*
21501290 TAAAAAATTAAAATTTATTAAAAATA
1 TAAAAAATT-AAATTTAATAAAAATA
21501316 TAAAAAA
1 TAAAAAA
21501323 ATTATAAAAT
Statistics
Matches: 54, Mismatches: 2, Indels: 8
0.84 0.03 0.12
Matches are distributed among these distances:
25 3 0.06
26 28 0.52
27 8 0.15
28 10 0.19
29 5 0.09
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (25 bp):
TAAAAAATTAAATTTAATAAAAATA
Found at i:21501505 original size:10 final size:10
Alignment explanation
Indices: 21501486--21501612 Score: 69
Period size: 9 Copynumber: 13.4 Consensus size: 10
21501476 TTTCAGTGCG
21501486 ATAA-TTTTT
1 ATAATTTTTT
21501495 ATAATTTTTT
1 ATAATTTTTT
*
21501505 ACGAA--TTTT
1 A-TAATTTTTT
21501514 AT-ATTTCTTT
1 ATAATTT-TTT
21501524 ATAA-TTTTT
1 ATAATTTTTT
21501533 ATAATTTTCTT
1 ATAATTTT-TT
**
21501544 ACGA--TTTT
1 ATAATTTTTT
**
21501552 ATAAAATTTT
1 ATAATTTTTT
21501562 ATAATTTTTCT
1 ATAATTTTT-T
21501573 AT-A-TTTTT
1 ATAATTTTTT
*
21501581 AT-ATATTTT
1 ATAATTTTTT
21501590 ATAATTTTTT
1 ATAATTTTTT
* *
21501600 CT-ATTTTTA
1 ATAATTTTTT
21501609 ATAA
1 ATAA
21501613 AATTTAAACA
Statistics
Matches: 91, Mismatches: 13, Indels: 27
0.69 0.10 0.21
Matches are distributed among these distances:
7 1 0.01
8 8 0.09
9 36 0.40
10 36 0.40
11 10 0.11
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.62
Consensus pattern (10 bp):
ATAATTTTTT
Found at i:21501515 original size:19 final size:19
Alignment explanation
Indices: 21501491--21501555 Score: 73
Period size: 19 Copynumber: 3.4 Consensus size: 19
21501481 GTGCGATAAT
21501491 TTTTATAATTTTTTACGAA
1 TTTTATAATTTTTTACGAA
*
21501510 TTTTAT-ATTTCTTTA-TAA
1 TTTTATAATTT-TTTACGAA
21501528 TTTTTATAATTTTCTTACG-A
1 -TTTTATAATTTT-TTACGAA
21501548 TTTTATAA
1 TTTTATAA
21501556 AATTTTATAA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
18 6 0.15
19 25 0.64
20 8 0.21
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.62
Consensus pattern (19 bp):
TTTTATAATTTTTTACGAA
Found at i:21501528 original size:38 final size:37
Alignment explanation
Indices: 21501486--21501593 Score: 121
Period size: 38 Copynumber: 2.8 Consensus size: 37
21501476 TTTCAGTGCG
**
21501486 ATAATTTTTATAATTTTTTACGAATTTTAT-ATTTCTTT
1 ATAATTTTTATAATTTTTTACG-ATTTTATAAAAT-TTT
21501524 ATAATTTTTATAATTTTCTTACGATTTTATAAAATTTT
1 ATAATTTTTATAATTTT-TTACGATTTTATAAAATTTT
* *
21501562 ATAATTTTTCTATATTTTTATA-TATTTTATAA
1 ATAATTTTTATA-ATTTTT-TACGATTTTATAA
21501594 TTTTTTCTAT
Statistics
Matches: 62, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
38 48 0.77
39 14 0.23
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (37 bp):
ATAATTTTTATAATTTTTTACGATTTTATAAAATTTT
Found at i:21501605 original size:9 final size:9
Alignment explanation
Indices: 21501510--21501607 Score: 56
Period size: 10 Copynumber: 10.3 Consensus size: 9
21501500 TTTTTACGAA
21501510 TTTTATATT
1 TTTTATATT
*
21501519 TCTTTATAAT
1 T-TTTATATT
21501529 TTTTATAATT
1 TTTTAT-ATT
*
21501539 TTCTTACGATT
1 TT-TTA-TATT
* **
21501550 TTATA-AAA
1 TTTTATATT
21501558 TTTTATAATT
1 TTTTAT-ATT
21501568 TTTCTATA-T
1 TTT-TATATT
*
21501577 TTTTATATA
1 TTTTATATT
21501586 TTTTATAATT
1 TTTTAT-ATT
*
21501596 TTTTCTATT
1 TTTTATATT
21501605 TTT
1 TTT
21501608 AATAAAATTT
Statistics
Matches: 68, Mismatches: 12, Indels: 18
0.69 0.12 0.18
Matches are distributed among these distances:
8 9 0.13
9 22 0.32
10 26 0.38
11 11 0.16
ACGTcount: A:0.28, C:0.05, G:0.01, T:0.66
Consensus pattern (9 bp):
TTTTATATT
Found at i:21502816 original size:24 final size:24
Alignment explanation
Indices: 21502755--21502817 Score: 99
Period size: 24 Copynumber: 2.6 Consensus size: 24
21502745 TAGACTAATA
*
21502755 AGAGTTTAACTCAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
* *
21502779 AGAGTTTAATTGAAACAATTAAAC
1 AGAGTTTAACTGAAACAAATAAAC
21502803 AGAGTTTAACTGAAA
1 AGAGTTTAACTGAAA
21502818 GATTATTTCT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.51, C:0.11, G:0.13, T:0.25
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAC
Found at i:21507001 original size:24 final size:24
Alignment explanation
Indices: 21506940--21507002 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
21506930 TAGACTAATA
* *
21506940 AGAGTTTGACTCAAACAAATAAAT
1 AGAGTTTAACTGAAACAAATAAAT
* *
21506964 AGAGTTTAATTGAAACAATTAAAT
1 AGAGTTTAACTGAAACAAATAAAT
21506988 AGAGTTTAACTGAAA
1 AGAGTTTAACTGAAA
21507003 GATTATTTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.49, C:0.08, G:0.14, T:0.29
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAT
Found at i:21507713 original size:21 final size:20
Alignment explanation
Indices: 21507687--21507738 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 20
21507677 TTGTTTTGGT
21507687 GTTGTTTTTTTTACTATTTTG
1 GTTGTTTTTTTT-CTATTTTG
*
21507708 GTTGTTGTTTTTTCTGTTTTG
1 GTTGTT-TTTTTTCTATTTTG
21507729 G-TGTTTTTTT
1 GTTGTTTTTTT
21507739 ATTGTTTTGG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 5 0.17
20 4 0.14
21 14 0.48
22 6 0.21
ACGTcount: A:0.04, C:0.04, G:0.19, T:0.73
Consensus pattern (20 bp):
GTTGTTTTTTTTCTATTTTG
Found at i:21507744 original size:19 final size:19
Alignment explanation
Indices: 21507692--21507749 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 19
21507682 TTGGTGTTGT
* *
21507692 TTTTTTTACTATTTTGGTTG
1 TTTTTTTATTGTTTTGG-TG
21507712 TTGTTTTT-TCTGTTTTGGTG
1 TT-TTTTTAT-TGTTTTGGTG
21507732 TTTTTTTATTGTTTTGGT
1 TTTTTTTATTGTTTTGGT
21507750 TACTGTTTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
19 14 0.42
20 7 0.21
21 12 0.36
ACGTcount: A:0.05, C:0.03, G:0.19, T:0.72
Consensus pattern (19 bp):
TTTTTTTATTGTTTTGGTG
Found at i:21507759 original size:52 final size:53
Alignment explanation
Indices: 21507688--21507791 Score: 122
Period size: 52 Copynumber: 2.0 Consensus size: 53
21507678 TGTTTTGGTG
** * * * *
21507688 TTGTTTTTTTTACTATTTTGGTTGTTGTTTTTT-CTGTTTTGGTGTT-TTTTTA
1 TTGTTTTGGTTACTATTTT-GATGCTGTTTTTTACTATTTTGATGTTGTTTTTA
*
21507740 TTGTTTTGGTTACTGTTTTGATGCTGTTTTTTACTATTTTGATGTTGTTTTT
1 TTGTTTTGGTTACTATTTTGATGCTGTTTTTTACTATTTTGATGTTGTTTTT
21507792 TCTGTTATTT
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
51 11 0.26
52 27 0.63
53 5 0.12
ACGTcount: A:0.08, C:0.05, G:0.18, T:0.69
Consensus pattern (53 bp):
TTGTTTTGGTTACTATTTTGATGCTGTTTTTTACTATTTTGATGTTGTTTTTA
Found at i:21507773 original size:21 final size:21
Alignment explanation
Indices: 21507749--21507797 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
21507739 ATTGTTTTGG
21507749 TTACTGTTTTGATGCTGTTTT
1 TTACTGTTTTGATGCTGTTTT
* *
21507770 TTACTATTTTGATGTTGTTTT
1 TTACTGTTTTGATGCTGTTTT
21507791 TT-CTGTT
1 TTACTGTT
21507798 ATTTTTGTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 4 0.16
21 21 0.84
ACGTcount: A:0.10, C:0.08, G:0.16, T:0.65
Consensus pattern (21 bp):
TTACTGTTTTGATGCTGTTTT
Found at i:21507797 original size:12 final size:11
Alignment explanation
Indices: 21507776--21507859 Score: 62
Period size: 12 Copynumber: 7.2 Consensus size: 11
21507766 TTTTTTACTA
*
21507776 TTTTGATGTTGT
1 TTTTGTTGTT-T
21507788 TTTT-TCTGTTAT
1 TTTTGT-TGTT-T
*
21507800 TTTTGTTGCTAT
1 TTTTGTTG-TTT
*
21507812 TTTAGTTGTTAT
1 TTTTGTTGTT-T
21507824 TTTTGTTGTTT
1 TTTTGTTGTTT
21507835 TTGTTGTTGTTT
1 TT-TTGTTGTTT
* *
21507847 TGTTGTTATTT
1 TTTTGTTGTTT
21507858 TT
1 TT
21507860 ATTGCTATTT
Statistics
Matches: 58, Mismatches: 9, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
11 13 0.22
12 43 0.74
13 2 0.03
ACGTcount: A:0.07, C:0.02, G:0.18, T:0.73
Consensus pattern (11 bp):
TTTTGTTGTTT
Found at i:21507803 original size:33 final size:32
Alignment explanation
Indices: 21507766--21507859 Score: 84
Period size: 33 Copynumber: 2.8 Consensus size: 32
21507756 TTTGATGCTG
21507766 TTTTTTACTATTTTGATGTTGTT-TTTTCTGTTAT
1 TTTTTTACTATTTT-A-GTTGTTATTTT-TGTTAT
* *
21507800 TTTTGTTGCTATTTTAGTTGTTATTTTTGTTGT
1 TTTT-TTACTATTTTAGTTGTTATTTTTGTTAT
** *
21507833 TTTTGTTGTTGTTTT-GTTGTTATTTTT
1 TTTT-TTACTATTTTAGTTGTTATTTTT
21507860 ATTGCTATTT
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
32 12 0.22
33 24 0.44
34 9 0.17
35 9 0.17
ACGTcount: A:0.09, C:0.03, G:0.16, T:0.72
Consensus pattern (32 bp):
TTTTTTACTATTTTAGTTGTTATTTTTGTTAT
Found at i:21507814 original size:24 final size:22
Alignment explanation
Indices: 21507782--21507858 Score: 81
Period size: 24 Copynumber: 3.5 Consensus size: 22
21507772 ACTATTTTGA
21507782 TGTTGT-TTTT-TCTGTTATTTT
1 TGTTGTATTTTGT-TGTTATTTT
21507803 TGTTGCTATTTTAGTTGTTATTTT
1 TGTTG-TATTTT-GTTGTTATTTT
*
21507827 TGTTGT-TTTTGTTGTT-GTTT
1 TGTTGTATTTTGTTGTTATTTT
21507847 TGTTGTTATTTT
1 TGTTG-TATTTT
21507859 TATTGCTATT
Statistics
Matches: 49, Mismatches: 1, Indels: 11
0.80 0.02 0.18
Matches are distributed among these distances:
20 8 0.16
21 12 0.24
22 9 0.18
23 5 0.10
24 14 0.29
25 1 0.02
ACGTcount: A:0.06, C:0.03, G:0.18, T:0.73
Consensus pattern (22 bp):
TGTTGTATTTTGTTGTTATTTT
Found at i:21507877 original size:32 final size:31
Alignment explanation
Indices: 21507811--21507900 Score: 94
Period size: 32 Copynumber: 2.9 Consensus size: 31
21507801 TTTGTTGCTA
* * *
21507811 TTTTAGTTGTTATTTTTGTTGTTTTTGTTGTTG
1 TTTT-GTTGTTATTTTTATTGCTATT-TTGTTG
21507844 TTTTGTTGTTATTTTTATTGCTATTTTGATTG
1 TTTTGTTGTTATTTTTATTGCTATTTTG-TTG
* *
21507876 TTTGGATGTTATTTTTA-TGC-ATTTT
1 TTTTGTTGTTATTTTTATTGCTATTTT
21507901 TACTATTGTT
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
30 5 0.10
31 6 0.12
32 36 0.71
33 4 0.08
ACGTcount: A:0.11, C:0.02, G:0.18, T:0.69
Consensus pattern (31 bp):
TTTTGTTGTTATTTTTATTGCTATTTTGTTG
Found at i:21521018 original size:37 final size:37
Alignment explanation
Indices: 21520971--21521045 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
21520961 CAATTGAATT
21520971 CAGGCCTGATTAAAAGATGACAATAACTCAATAAACC
1 CAGGCCTGATTAAAAGATGACAATAACTCAATAAACC
21521008 CAGGCCTGATTAAAAGATGACAATAACTCAATAAACC
1 CAGGCCTGATTAAAAGATGACAATAACTCAATAAACC
21521045 C
1 C
21521046 TTTAAATAGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.45, C:0.23, G:0.13, T:0.19
Consensus pattern (37 bp):
CAGGCCTGATTAAAAGATGACAATAACTCAATAAACC
Found at i:21521125 original size:29 final size:30
Alignment explanation
Indices: 21521093--21521149 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
21521083 TTGATTTAAT
*
21521093 GTGTAATTATATACATG-AACTTTAATTTG
1 GTGTAATTATATACATGAAACTCTAATTTG
*
21521122 GTGTAATTATATACGTGAAACTCTAATT
1 GTGTAATTATATACATGAAACTCTAATT
21521150 GTAGTTCAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 16 0.64
30 9 0.36
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.42
Consensus pattern (30 bp):
GTGTAATTATATACATGAAACTCTAATTTG
Found at i:21524009 original size:15 final size:15
Alignment explanation
Indices: 21523991--21524037 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
21523981 TTTTCTCAGA
21523991 TTATATTTTAATCAC
1 TTATATTTTAATCAC
* *
21524006 TTATATTTGAAACAC
1 TTATATTTTAATCAC
*
21524021 -TATATTTTAATTAC
1 TTATATTTTAATCAC
21524035 TTA
1 TTA
21524038 CGTTATCATT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
14 11 0.42
15 15 0.58
ACGTcount: A:0.36, C:0.11, G:0.02, T:0.51
Consensus pattern (15 bp):
TTATATTTTAATCAC
Found at i:21534654 original size:92 final size:92
Alignment explanation
Indices: 21534494--21534702 Score: 400
Period size: 92 Copynumber: 2.3 Consensus size: 92
21534484 ATAAGTAGAA
*
21534494 ATATAGATTAATTTGATAACACAAACCCAAAAAGGTTAATTAAAACATAATATAAACAATAGTAA
1 ATATAGATTAATTTGATAACACAAACCCAAAAAGATTAATTAAAACATAATATAAACAATAGTAA
21534559 TATTAAATAGGGTATAAAATATTTTAG
66 TATTAAATAGGGTATAAAATATTTTAG
*
21534586 ATATAGATTAATTTGATAACACAAACCCAAAAAGATTAATTAAAACATAATATAAACAATAGTCA
1 ATATAGATTAATTTGATAACACAAACCCAAAAAGATTAATTAAAACATAATATAAACAATAGTAA
21534651 TATTAAATAGGGTATAAAATATTTTAG
66 TATTAAATAGGGTATAAAATATTTTAG
21534678 ATATAGATTAATTTGATAACACAAA
1 ATATAGATTAATTTGATAACACAAA
21534703 ATAAATACTC
Statistics
Matches: 115, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
92 115 1.00
ACGTcount: A:0.52, C:0.08, G:0.09, T:0.31
Consensus pattern (92 bp):
ATATAGATTAATTTGATAACACAAACCCAAAAAGATTAATTAAAACATAATATAAACAATAGTAA
TATTAAATAGGGTATAAAATATTTTAG
Found at i:21538561 original size:16 final size:17
Alignment explanation
Indices: 21538531--21538563 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
21538521 TTTTTAGATT
*
21538531 ATTTTTTATTTAAAATA
1 ATTTTTTATTAAAAATA
21538548 ATTTTTTA-TAAAAATA
1 ATTTTTTATTAAAAATA
21538564 TAGTACAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
ATTTTTTATTAAAAATA
Found at i:21541450 original size:7 final size:7
Alignment explanation
Indices: 21541433--21541465 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
21541423 AAAAGAATAC
21541433 CTGAA-G
1 CTGAAGG
21541439 CTGAAGG
1 CTGAAGG
21541446 CTGAAGG
1 CTGAAGG
21541453 CTGAAGG
1 CTGAAGG
21541460 CTGAAG
1 CTGAAG
21541466 CAGTAAACCA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 5 0.19
7 21 0.81
ACGTcount: A:0.30, C:0.15, G:0.39, T:0.15
Consensus pattern (7 bp):
CTGAAGG
Found at i:21543878 original size:15 final size:15
Alignment explanation
Indices: 21543860--21543917 Score: 59
Period size: 15 Copynumber: 4.0 Consensus size: 15
21543850 TAAGATAAAT
21543860 TTAAAATATTTTTAA
1 TTAAAATATTTTTAA
**
21543875 TTAAAATAATAGTT--
1 TTAAAAT-ATTTTTAA
21543889 TT-AAATATTTTTAA
1 TTAAAATATTTTTAA
*
21543903 TTAAAATATTATTAA
1 TTAAAATATTTTTAA
21543918 ATATTCAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
12 4 0.12
13 4 0.12
14 4 0.12
15 18 0.53
16 4 0.12
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (15 bp):
TTAAAATATTTTTAA
Found at i:21544955 original size:19 final size:20
Alignment explanation
Indices: 21544905--21544956 Score: 54
Period size: 19 Copynumber: 2.6 Consensus size: 20
21544895 CAATACATTA
* *
21544905 AATT-AAAAAAATAACCCTT
1 AATTAAAAAAAATAACACGT
*
21544924 AATTTAAAGAAAATAA-ACGT
1 AA-TTAAAAAAAATAACACGT
21544944 AATTAAAAAAAAT
1 AATTAAAAAAAAT
21544957 GTGATAAGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
19 12 0.44
20 6 0.22
21 9 0.33
ACGTcount: A:0.63, C:0.08, G:0.04, T:0.25
Consensus pattern (20 bp):
AATTAAAAAAAATAACACGT
Found at i:21550633 original size:6 final size:6
Alignment explanation
Indices: 21550624--21550651 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
21550614 TATATTTATC
21550624 AAATAT AAATAT AAATAT AAATAT AAAT
1 AAATAT AAATAT AAATAT AAATAT AAAT
21550652 TGATGTATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
AAATAT
Found at i:21551068 original size:15 final size:14
Alignment explanation
Indices: 21551050--21551084 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
21551040 ATATAATATG
21551050 ATAAAATAATTAAAA
1 ATAAAATAA-TAAAA
21551065 ATAAAAATAATAAAA
1 AT-AAAATAATAAAA
21551080 ATAAA
1 ATAAA
21551085 TAAATATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 3 0.16
15 9 0.47
16 7 0.37
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (14 bp):
ATAAAATAATAAAA
Found at i:21551491 original size:17 final size:17
Alignment explanation
Indices: 21551471--21551503 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
21551461 ATTAAAGCAA
21551471 ATAATAAAT-TAATATCG
1 ATAAT-AATCTAATATCG
21551488 ATAATAATCTAATATC
1 ATAATAATCTAATATC
21551504 CAAATTCATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.52, C:0.09, G:0.03, T:0.36
Consensus pattern (17 bp):
ATAATAATCTAATATCG
Found at i:21553022 original size:33 final size:33
Alignment explanation
Indices: 21552960--21553022 Score: 76
Period size: 33 Copynumber: 1.9 Consensus size: 33
21552950 AAATAAGGGT
*
21552960 TAATTATAATATTAGCTAAGAATTCAAATTCAC
1 TAATTATAATATTAGCTAAGAATTAAAATTCAC
*
21552993 TAATTATAAATATTTAGC-AAGTA-TAAAATT
1 TAATTAT-AATA-TTAGCTAAGAATTAAAATT
21553023 TGATCCTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
33 13 0.50
34 8 0.31
35 5 0.19
ACGTcount: A:0.48, C:0.08, G:0.06, T:0.38
Consensus pattern (33 bp):
TAATTATAATATTAGCTAAGAATTAAAATTCAC
Found at i:21554218 original size:15 final size:16
Alignment explanation
Indices: 21554182--21554221 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
21554172 ATAATAAAAA
21554182 TATAATTTTATCATTTT
1 TATAA-TTTATCATTTT
*
21554199 AATAATTTAT-ATTTT
1 TATAATTTATCATTTT
21554214 TATAATTT
1 TATAATTT
21554222 TTAAAGGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 12 0.57
16 5 0.24
17 4 0.19
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (16 bp):
TATAATTTATCATTTT
Found at i:21559472 original size:15 final size:15
Alignment explanation
Indices: 21559452--21559482 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
21559442 TATTATTCGA
21559452 AAGTCTTGACCACTC
1 AAGTCTTGACCACTC
21559467 AAGTCTTGACCACTC
1 AAGTCTTGACCACTC
21559482 A
1 A
21559483 GATCATCATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.29, C:0.32, G:0.13, T:0.26
Consensus pattern (15 bp):
AAGTCTTGACCACTC
Found at i:21560006 original size:15 final size:15
Alignment explanation
Indices: 21559982--21560012 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
21559972 GTTTTTAAGT
21559982 TTATAATATTTTATA
1 TTATAATATTTTATA
*
21559997 TTATATTATTTTATA
1 TTATAATATTTTATA
21560012 T
1 T
21560013 ATTATGTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TTATAATATTTTATA
Found at i:21561741 original size:22 final size:21
Alignment explanation
Indices: 21561697--21561741 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
21561687 TCTTTTCACC
* *
21561697 ATTTTTAAATATAAAATATTT
1 ATTTTTAAATATAAAAAAATT
*
21561718 ATTTTTATATTATAAAAAAATT
1 ATTTTTA-AATATAAAAAAATT
21561740 AT
1 AT
21561742 AAAATATTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
ATTTTTAAATATAAAAAAATT
Found at i:21565755 original size:2 final size:2
Alignment explanation
Indices: 21565748--21565782 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
21565738 TAACGGAGCA
21565748 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21565783 TGATCTACTT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:21569690 original size:29 final size:28
Alignment explanation
Indices: 21569634--21569733 Score: 91
Period size: 29 Copynumber: 3.6 Consensus size: 28
21569624 TTTGATCTTT
* * *
21569634 TAAAATGAAAAATTAATTTAATTTTTAA
1 TAAAATTATAAATTAATTTAATATTTAA
21569662 TAAAATTATAAATTATATTTAATATTTAA
1 TAAAATTATAAATTA-ATTTAATATTTAA
* * *
21569691 TTAAATT-TAATATTAATTT-TTA-TAAA
1 TAAAATTATAA-ATTAATTTAATATTTAA
21569717 TAAAAATTAT-AATTAAT
1 T-AAAATTATAAATTAAT
21569734 ATATAAAATA
Statistics
Matches: 61, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
26 10 0.16
27 8 0.13
28 21 0.34
29 22 0.36
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (28 bp):
TAAAATTATAAATTAATTTAATATTTAA
Found at i:21569698 original size:17 final size:16
Alignment explanation
Indices: 21569672--21569708 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
21569662 TAAAATTATA
*
21569672 AATTATATTTAATATTT
1 AATTAAATTTAATA-TT
21569689 AATTAAATTTAATATT
1 AATTAAATTTAATATT
21569705 AATT
1 AATT
21569709 TTTATAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
AATTAAATTTAATATT
Found at i:21570484 original size:11 final size:11
Alignment explanation
Indices: 21570468--21570501 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
21570458 TATATATATT
*
21570468 TAAAAATTATA
1 TAAAAATAATA
21570479 TAAAAATAATA
1 TAAAAATAATA
*
21570490 TAAAATTAATA
1 TAAAAATAATA
21570501 T
1 T
21570502 GAACGGATCG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
TAAAAATAATA
Found at i:21581954 original size:15 final size:17
Alignment explanation
Indices: 21581933--21581973 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
21581923 TAATCTTCTA
21581933 AAAATTATAAAAAT-AT
1 AAAATTATAAAAATAAT
*
21581949 -AAATTATTAAAATAAT
1 AAAATTATAAAAATAAT
21581965 AAAATTATA
1 AAAATTATA
21581974 TTTTTACTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 12 0.57
16 2 0.10
17 7 0.33
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AAAATTATAAAAATAAT
Found at i:21597567 original size:17 final size:15
Alignment explanation
Indices: 21597547--21597601 Score: 53
Period size: 17 Copynumber: 3.6 Consensus size: 15
21597537 TTTATTTTGG
21597547 ATTTAAATTTGTATACA
1 ATTTAAATTT-TATA-A
21597564 ATTTAAATCTATTATAA
1 ATTTAAAT-T-TTATAA
21597581 ATTTAAA-TTTA-AA
1 ATTTAAATTTTATAA
21597594 A-TTAAATT
1 ATTTAAATT
21597602 AAATGTCCAT
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
12 5 0.14
13 4 0.11
14 3 0.09
15 1 0.03
17 16 0.46
18 5 0.14
19 1 0.03
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (15 bp):
ATTTAAATTTTATAA
Found at i:21598393 original size:21 final size:21
Alignment explanation
Indices: 21598356--21598395 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
21598346 GCTAAGAACA
*
21598356 TTAATATTTTCATTAATAATT
1 TTAATATTTTCAATAATAATT
21598377 TTAATCATTTT-AATAATAA
1 TTAAT-ATTTTCAATAATAA
21598396 CAGATACAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (21 bp):
TTAATATTTTCAATAATAATT
Found at i:21599533 original size:28 final size:29
Alignment explanation
Indices: 21599494--21599764 Score: 170
Period size: 29 Copynumber: 9.4 Consensus size: 29
21599484 GGACTGTCCA
21599494 AAAATTACCATTTTACCCCCAAACTTT-CC
1 AAAATTACCATTTTACCCCCAAA-TTTACC
**
21599523 AAAA-TACCATTTTCAACCCCCCGATTTCACC
1 AAAATTACCATTTT--ACCCCCAAATTT-ACC
* * *
21599554 AAAAATTACCGTTTTACCCCTAAATTTTCC
1 -AAAATTACCATTTTACCCCCAAATTTACC
* * * * *
21599584 AAAA-TCCCATTTTTAACCTCGATTTTACC
1 AAAATTACCA-TTTTACCCCCAAATTTACC
* *
21599613 AAAATTACCATTTTACCCCCGAATTTCCC
1 AAAATTACCATTTTACCCCCAAATTTACC
* * *
21599642 AAAA-T-CCTATTTTAACCTC-GATTTCACC
1 AAAATTACC-ATTTTACCCCCAAATTT-ACC
*
21599670 AAAAATTACCATTTTACCCCTAAACTTT-CC
1 -AAAATTACCATTTTACCCCCAAA-TTTACC
* * * *
21599700 AAAA-TCCCATTTTTAACCCC-GATTCACC
1 AAAATTACCA-TTTTACCCCCAAATTTACC
*
21599728 AAAATT-CCATTTT-CCCCCAAATTCACC
1 AAAATTACCATTTTACCCCCAAATTTACC
21599755 AAAATT-CCAT
1 AAAATTACCAT
21599765 ACCCCCCTAA
Statistics
Matches: 188, Mismatches: 35, Indels: 40
0.71 0.13 0.15
Matches are distributed among these distances:
26 4 0.02
27 29 0.15
28 38 0.20
29 64 0.34
30 24 0.13
31 14 0.07
32 7 0.04
33 8 0.04
ACGTcount: A:0.34, C:0.32, G:0.02, T:0.32
Consensus pattern (29 bp):
AAAATTACCATTTTACCCCCAAATTTACC
Found at i:21599638 original size:58 final size:59
Alignment explanation
Indices: 21599491--21599764 Score: 344
Period size: 58 Copynumber: 4.7 Consensus size: 59
21599481 CTTGGACTGT
* * *
21599491 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATACCATTTTCAACCCCCCGATTTCA
1 CCAAAAATTACCATTTTACCCCCAAATTTTCCAAAATCCCATTTTTAA--CCCCGATTTCA
* * * *
21599552 CCAAAAATTACCGTTTTACCCCTAAATTTTCCAAAATCCCATTTTTAACCTCGATTTTA
1 CCAAAAATTACCATTTTACCCCCAAATTTTCCAAAATCCCATTTTTAACCCCGATTTCA
* * * *
21599611 CC-AAAATTACCATTTTACCCCCGAATTTCCCAAAATCCTA-TTTTAACCTCGATTTCA
1 CCAAAAATTACCATTTTACCCCCAAATTTTCCAAAATCCCATTTTTAACCCCGATTTCA
* *
21599668 CCAAAAATTACCATTTTACCCCTAAACTTTCCAAAATCCCATTTTTAACCCCGA-TTCA
1 CCAAAAATTACCATTTTACCCCCAAATTTTCCAAAATCCCATTTTTAACCCCGATTTCA
** *
21599726 CC-AAAATT-CCATTTT-CCCCCAAATTCACCAAAATTCCAT
1 CCAAAAATTACCATTTTACCCCCAAATTTTCCAAAATCCCAT
21599765 ACCCCCCTAA
Statistics
Matches: 187, Mismatches: 24, Indels: 10
0.85 0.11 0.05
Matches are distributed among these distances:
55 19 0.10
56 7 0.04
57 24 0.13
58 72 0.39
59 22 0.12
61 43 0.23
ACGTcount: A:0.34, C:0.32, G:0.02, T:0.32
Consensus pattern (59 bp):
CCAAAAATTACCATTTTACCCCCAAATTTTCCAAAATCCCATTTTTAACCCCGATTTCA
Found at i:21599770 original size:26 final size:27
Alignment explanation
Indices: 21599721--21599790 Score: 81
Period size: 27 Copynumber: 2.6 Consensus size: 27
21599711 TTTAACCCCG
**
21599721 ATTCACCAAAATTCCATTTTCCCCC-AA
1 ATTCACCAAAATTCCA-TACCCCCCTAA
21599748 ATTCACCAAAATTCCATACCCCCCTAA
1 ATTCACCAAAATTCCATACCCCCCTAA
* *
21599775 ATT-TCTAAAATTCCAT
1 ATTCACCAAAATTCCAT
21599791 TTTTAACCTC
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
26 17 0.45
27 21 0.55
ACGTcount: A:0.36, C:0.34, G:0.00, T:0.30
Consensus pattern (27 bp):
ATTCACCAAAATTCCATACCCCCCTAA
Found at i:21603368 original size:25 final size:25
Alignment explanation
Indices: 21603340--21603387 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
21603330 ATATTTTTTT
21603340 ATTTTAATAT-TTAATAATTTTATAC
1 ATTTTAATATATTAA-AATTTTATAC
* *
21603365 ATTTTTATTTATTAAAATTTTAT
1 ATTTTAATATATTAAAATTTTAT
21603388 CTAGTCATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 16 0.80
26 4 0.20
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (25 bp):
ATTTTAATATATTAAAATTTTATAC
Found at i:21613962 original size:29 final size:29
Alignment explanation
Indices: 21613920--21613979 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
21613910 AAGATTTAGG
21613920 TATGTCACACCATGAACGTCACAAGTGAA
1 TATGTCACACCATGAACGTCACAAGTGAA
21613949 TATGTCACACCATGAACGTCACAAGTGAA
1 TATGTCACACCATGAACGTCACAAGTGAA
21613978 TA
1 TA
21613980 AATCTATAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.22
Consensus pattern (29 bp):
TATGTCACACCATGAACGTCACAAGTGAA
Found at i:21614885 original size:88 final size:85
Alignment explanation
Indices: 21614745--21614923 Score: 209
Period size: 88 Copynumber: 2.1 Consensus size: 85
21614735 CAAAACAAGT
* *
21614745 AATTAAGTCTCTCTTTTTTTGTATTCACTTGAGTACTTAAAATTTCAAAATGCATAAAAAATG-T
1 AATTAAGTCTCTCTTTTTTTGTACTCAATTGAGTACTTAAAATTTCAAAATGCATAAAAAA-GAT
* * *
21614809 CTTCAAACCTTTT-CAAAAAGC
65 CCTCAAA-CTTTTAAAAAAAAC
* * * * *
21614830 AATTAAGTCTCTATCTTTTTTTTTCACTCAATTGAGTACTTGAACTTTTAAAATGCATCAAAAAG
1 AATTAAGTCTC--TCTTTTTTTGT-ACTCAATTGAGTACTTAAAATTTCAAAATGCATAAAAAAG
21614895 ATCCTCAAACTTTTAAAAAAAAC
63 ATCCTCAAACTTTTAAAAAAAAC
21614918 AATTAA
1 AATTAA
21614924 ACCCCTACTT
Statistics
Matches: 79, Mismatches: 10, Indels: 7
0.82 0.10 0.07
Matches are distributed among these distances:
85 11 0.14
87 16 0.20
88 52 0.66
ACGTcount: A:0.39, C:0.16, G:0.07, T:0.38
Consensus pattern (85 bp):
AATTAAGTCTCTCTTTTTTTGTACTCAATTGAGTACTTAAAATTTCAAAATGCATAAAAAAGATC
CTCAAACTTTTAAAAAAAAC
Found at i:21615383 original size:38 final size:38
Alignment explanation
Indices: 21615298--21615384 Score: 97
Period size: 37 Copynumber: 2.3 Consensus size: 38
21615288 TTTCAATGCA
** **
21615298 TTTTATAATTTTTTTATGATTTCTATAAAATTTTACAAT
1 TTTTAT-ATTTTTTTACAATTTCTATAAAAAATTACAAT
*
21615337 TTTT-TATTTTTTTACAATTTTTATAAAAAAATTA-AAT
1 TTTTATATTTTTTTACAATTTCTAT-AAAAAATTACAAT
21615374 TTTTATATTTT
1 TTTTATATTTT
21615385 ATTAAAAATT
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
37 23 0.56
38 14 0.34
39 4 0.10
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.61
Consensus pattern (38 bp):
TTTTATATTTTTTTACAATTTCTATAAAAAATTACAAT
Found at i:21615416 original size:22 final size:23
Alignment explanation
Indices: 21615388--21615432 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
21615378 ATATTTTATT
21615388 AAAAATTAATAA-TTTTTCTAAA
1 AAAAATTAATAACTTTTTCTAAA
*
21615410 AAAAATTTATAACTTTTTTCTAA
1 AAAAATTAATAAC-TTTTTCTAA
21615433 TTTTTAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 11 0.55
24 9 0.45
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (23 bp):
AAAAATTAATAACTTTTTCTAAA
Found at i:21615605 original size:89 final size:89
Alignment explanation
Indices: 21615460--21615662 Score: 273
Period size: 89 Copynumber: 2.3 Consensus size: 89
21615450 GGTTTAATTG
* * * * **
21615460 TTTTTGAAAAATTTTGAGGG-TCTTTTTTATGTATTTTGAAAGTTCAAGTACCCAATTGAGTGGG
1 TTTTTGAAAAAATTTGAGGGTTTTTTTTTATGCATTTTGAAAGCTCAAGTACCCAATTGAGTGCA
** **
21615524 AAAAAAAGCGGGGCTTAATTGCTT
66 AAAAAAAGAAGAACTTAATTGCTT
* * *
21615548 TTTTTGAAGAAGTTTGAGGGTTTTTTTTTATGCATTTTGAAAGCTCAAGTACTCAATTGAGTGCA
1 TTTTTGAAAAAATTTGAGGGTTTTTTTTTATGCATTTTGAAAGCTCAAGTACCCAATTGAGTGCA
21615613 AAAAAAAGAAGAACTTAATTGCTT
66 AAAAAAAGAAGAACTTAATTGCTT
*
21615637 TTTTTGAAAAAATTTGAGGATTTTTT
1 TTTTTGAAAAAATTTGAGGGTTTTTT
21615663 ACACCTTTAA
Statistics
Matches: 99, Mismatches: 15, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
88 18 0.18
89 81 0.82
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.40
Consensus pattern (89 bp):
TTTTTGAAAAAATTTGAGGGTTTTTTTTTATGCATTTTGAAAGCTCAAGTACCCAATTGAGTGCA
AAAAAAAGAAGAACTTAATTGCTT
Found at i:21616350 original size:42 final size:42
Alignment explanation
Indices: 21616302--21616387 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
21616292 ATAAAGCACC
21616302 ATAGACATTAGGTTTTGTTGGTTGGAATAGAATAAAGTTCCA
1 ATAGACATTAGGTTTTGTTGGTTGGAATAGAATAAAGTTCCA
21616344 ATAGACATTAGGTTTTGTTGGTTGGAATAGAATAAAGTTCCA
1 ATAGACATTAGGTTTTGTTGGTTGGAATAGAATAAAGTTCCA
21616386 AT
1 AT
21616388 GAAATAGTTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.34, C:0.07, G:0.23, T:0.36
Consensus pattern (42 bp):
ATAGACATTAGGTTTTGTTGGTTGGAATAGAATAAAGTTCCA
Found at i:21616586 original size:14 final size:14
Alignment explanation
Indices: 21616547--21616587 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
21616537 TACTCTTTCA
21616547 AATTTTAAAA-TTT
1 AATTTTAAAATTTT
* *
21616560 AATTTTTATATTTT
1 AATTTTAAAATTTT
21616574 AATTTTAAAATTTT
1 AATTTTAAAATTTT
21616588 GAATCACTGT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
13 8 0.35
14 15 0.65
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
AATTTTAAAATTTT
Found at i:21620877 original size:24 final size:24
Alignment explanation
Indices: 21620822--21620877 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
21620812 TTAATTTTCG
21620822 GTTAATAATTAATTCGATTAAAAA
1 GTTAATAATTAATTCGATTAAAAA
* * **
21620846 CTTGATAATTAATT-GAATTAACTA
1 GTTAATAATTAATTCG-ATTAAAAA
21620870 GTTAATAA
1 GTTAATAA
21620878 AAAATATTAA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
23 1 0.04
24 24 0.96
ACGTcount: A:0.46, C:0.05, G:0.09, T:0.39
Consensus pattern (24 bp):
GTTAATAATTAATTCGATTAAAAA
Found at i:21623253 original size:30 final size:30
Alignment explanation
Indices: 21623156--21623330 Score: 182
Period size: 30 Copynumber: 6.0 Consensus size: 30
21623146 CGTGAAATCG
*
21623156 GGGGTAAAAATGA-AATTTTAG-AAAGTTTT
1 GGGGTTAAAAT-ATAATTTTAGAAAAGTTTT
* * *
21623185 GAGGTCAAAATA-AA-TTTAGAAAAGTTTA
1 GGGGTTAAAATATAATTTTAGAAAAGTTTT
*
21623213 GGGGTCAAAATATAATTTATAGAAAA-TTTT
1 GGGGTTAAAATATAATTT-TAGAAAAGTTTT
* *
21623243 GGGGTTAAAATATAATTTTGGAAAAGTTTA
1 GGGGTTAAAATATAATTTTAGAAAAGTTTT
* * *
21623273 GAGGTTAAAATGTAA-TTTAAAAAAGTTTT
1 GGGGTTAAAATATAATTTTAGAAAAGTTTT
* *
21623302 AGGGTTAAAATATAATTTTGGAAAAGTTT
1 GGGGTTAAAATATAATTTTAGAAAAGTTT
21623331 AAGGGTCAAA
Statistics
Matches: 122, Mismatches: 18, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
27 5 0.04
28 21 0.17
29 40 0.33
30 49 0.40
31 7 0.06
ACGTcount: A:0.43, C:0.01, G:0.20, T:0.35
Consensus pattern (30 bp):
GGGGTTAAAATATAATTTTAGAAAAGTTTT
Found at i:21623316 original size:59 final size:58
Alignment explanation
Indices: 21623162--21623349 Score: 213
Period size: 59 Copynumber: 3.2 Consensus size: 58
21623152 ATCGGGGGTA
* * * * * *
21623162 AAAATGAAATTTTAGAAAGTTTTGAGGTCAAAATA-AA-TTTAGAAAAGTTTAGGGGTC
1 AAAATGTAATTTAAAAAAGTTTTG-GGTTAAAATATAATTTTGGAAAAGTTTAGAGGTC
* *
21623219 AAAATATAATTTATAGAAAA-TTTTGGGGTTAAAATATAATTTTGGAAAAGTTTAGAGGTT
1 AAAATGTAATTTA-A-AAAAGTTTT-GGGTTAAAATATAATTTTGGAAAAGTTTAGAGGTC
21623279 AAAATGTAATTTAAAAAAGTTTTAGGGTTAAAATATAATTTTGGAAAAGTTTA-AGGGTC
1 AAAATGTAATTTAAAAAAGTTTT-GGGTTAAAATATAATTTTGGAAAAGTTTAGA-GGTC
*
21623338 AAAATGTCATTT
1 AAAATGTAATTT
21623350 TTGGATAGTT
Statistics
Matches: 112, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
57 10 0.09
58 19 0.17
59 54 0.48
60 29 0.26
ACGTcount: A:0.44, C:0.02, G:0.19, T:0.36
Consensus pattern (58 bp):
AAAATGTAATTTAAAAAAGTTTTGGGTTAAAATATAATTTTGGAAAAGTTTAGAGGTC
Found at i:21623362 original size:89 final size:88
Alignment explanation
Indices: 21623169--21623342 Score: 210
Period size: 89 Copynumber: 2.0 Consensus size: 88
21623159 GTAAAAATGA
* * *
21623169 AATTTTAG-AAAGTTTTGAGGTCAAAATAAATTTAGAAAAGTTTAGGGGTCAAAATATAATTTAT
1 AATTTTGGAAAAGTTTAGAGGTCAAAATAAATTTAAAAAAGTTTAGGGGTCAAAATATAATTTAT
** *
21623233 AGAAAATTTTGGGGTTAAAATAT
66 AGAAAATTTAAGGGTCAAAATAT
* * *
21623256 AATTTTGGAAAAGTTTAGAGGTTAAAATGTAATTTAAAAAAGTTTTA-GGGTTAAAATATAATTT
1 AATTTTGGAAAAGTTTAGAGGTCAAAAT-AAATTTAAAAAAG-TTTAGGGGTCAAAATATAATTT
*
21623320 -TGGAAAAGTTTAAGGGTCAAAAT
64 ATAGAAAA-TTTAAGGGTCAAAAT
21623343 GTCATTTTTG
Statistics
Matches: 73, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
87 7 0.10
88 23 0.32
89 39 0.53
90 4 0.05
ACGTcount: A:0.44, C:0.02, G:0.19, T:0.36
Consensus pattern (88 bp):
AATTTTGGAAAAGTTTAGAGGTCAAAATAAATTTAAAAAAGTTTAGGGGTCAAAATATAATTTAT
AGAAAATTTAAGGGTCAAAATAT
Found at i:21624453 original size:21 final size:21
Alignment explanation
Indices: 21624429--21624478 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
21624419 TTTATTACAT
*
21624429 TATTACTAATTTTATTAATAA
1 TATTAATAATTTTATTAATAA
* *
21624450 TATTAATATTTTTATTAATACT
1 TATTAATAATTTTATTAATA-A
21624472 TATTAAT
1 TATTAAT
21624479 GCTATTTACT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 18 0.72
22 7 0.28
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (21 bp):
TATTAATAATTTTATTAATAA
Found at i:21624525 original size:22 final size:22
Alignment explanation
Indices: 21624497--21624541 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
21624487 CTGCTAACAT
* *
21624497 TTATTATTACTGTTATTACTAA
1 TTATTATTAATATTATTACTAA
*
21624519 TTATTATTAATATTATTATTAA
1 TTATTATTAATATTATTACTAA
21624541 T
1 T
21624542 AGGTATTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (22 bp):
TTATTATTAATATTATTACTAA
Found at i:21625327 original size:7 final size:6
Alignment explanation
Indices: 21625283--21625346 Score: 53
Period size: 6 Copynumber: 11.0 Consensus size: 6
21625273 TTTATAATAT
* * *
21625283 TTTAAA TTCAAA -TTAAA TTCAAA TTTAAA -ATAAA TTTAAA TTTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA -TTTAAA
* *
21625330 -ATAAA TTTAAT TTTAAA
1 TTTAAA TTTAAA TTTAAA
21625347 ACAAATTCAA
Statistics
Matches: 44, Mismatches: 10, Indels: 8
0.71 0.16 0.13
Matches are distributed among these distances:
5 12 0.27
6 26 0.59
7 6 0.14
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (6 bp):
TTTAAA
Found at i:21625327 original size:18 final size:17
Alignment explanation
Indices: 21625283--21625353 Score: 88
Period size: 17 Copynumber: 4.1 Consensus size: 17
21625273 TTTATAATAT
* *
21625283 TTTAAATTCAAATTAAA
1 TTTAAATTTAAAATAAA
*
21625300 TTCAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
21625317 TTTAAATTTTAAAATAAA
1 TTTAAA-TTTAAAATAAA
* *
21625335 TTTAATTTTAAAACAAA
1 TTTAAATTTAAAATAAA
21625352 TT
1 TT
21625354 CAAAATGGTT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
17 31 0.66
18 16 0.34
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:21626213 original size:206 final size:200
Alignment explanation
Indices: 21625701--21626234 Score: 687
Period size: 201 Copynumber: 2.6 Consensus size: 200
21625691 CTTGGCCCCA
* * * * * * * *
21625701 TTCTCAGTGTCTCATCAGGAAGGTGACTGCATCGTTTGTTTTGATCCACTTCTCTGTG-TTTCAA
1 TTCTCTGTGTCTCATCAGGAAGATGACCGCCTC-TTTGTTTTAATTCGCTTCTCTG-GATCTC-A
* * * * * *
21625765 T-AGGAAGACGGATTTGGTTCACTTCTCTGTGGCTCATCAGAAAGCTAACCATTTTATTGCTTCT
63 TCAGGAAGACGAATTTGGTCCACTTCTCAGTGTCTCATCAGGAAGCTAACCATTTTATTGCTTCA
21625829 ACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCGCATCAATCGTCGAGT
128 ACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCGCATCAATCGTCGAGT
21625894 TGGCATAC
193 TGGCATAC
* * * * * *
21625902 TTCTCTGTATCTTATCAAGAAGATGACCGCCTCTTTTTTTTCAATTCGTTTCTCTGGATCTCTTC
1 TTCTCTGTGTCTCATCAGGAAGATGACCGCCTCTTTGTTTT-AATTCGCTTCTCTGGATCTCATC
*
21625967 AGGAAGACGAATTTGGTCCACTTCTCAGTGTCTCATCAGGAAGATAACCATTTTATTGCTTCAAC
65 AGGAAGACGAATTTGGTCCACTTCTCAGTGTCTCATCAGGAAGCTAACCATTTTATTGCTTCAAC
* * * *
21626032 CTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCGCATTGAGCCTGGGTTTG
130 CTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCGCA-TCA--AT-CG-TCG
* *
21626097 ATTTGGTC-TTC
190 AGTTGG-CATAC
*
21626108 TTCTCTGTGTCTCATCAGGAAGATGACCGCCTCATTTGTTTTAATTCGCTTCTCTGGATCTCCTC
1 TTCTCTGTGTCTCATCAGGAAGATGACCGCCTC-TTTGTTTTAATTCGCTTCTCTGGATCTCATC
*
21626173 AGGAAGACGAATTTGGTCCACTTCTCAGTGTCTTATCAGGAAGCTAACCATTTTATTGCTTC
65 AGGAAGACGAATTTGGTCCACTTCTCAGTGTCTCATCAGGAAGCTAACCATTTTATTGCTTC
21626235 GAAATTTAAT
Statistics
Matches: 288, Mismatches: 35, Indels: 15
0.85 0.10 0.04
Matches are distributed among these distances:
200 9 0.03
201 147 0.51
202 2 0.01
204 1 0.00
205 1 0.00
206 120 0.42
207 8 0.03
ACGTcount: A:0.21, C:0.23, G:0.20, T:0.36
Consensus pattern (200 bp):
TTCTCTGTGTCTCATCAGGAAGATGACCGCCTCTTTGTTTTAATTCGCTTCTCTGGATCTCATCA
GGAAGACGAATTTGGTCCACTTCTCAGTGTCTCATCAGGAAGCTAACCATTTTATTGCTTCAACC
TGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCGCATCAATCGTCGAGTTGG
CATAC
Found at i:21626962 original size:201 final size:205
Alignment explanation
Indices: 21626669--21627138 Score: 666
Period size: 201 Copynumber: 2.3 Consensus size: 205
21626659 GTGTTTCAAT
* * * * * *
21626669 AGGAAGACGGATTTGGTTCACTTCTCTGTGGCTCATCAGAAAGCTAACCATTTTATTGCTTCTAC
1 AGGAAGACGAATTTGGTCCACTTCTCAGTGTCTCATCAGGAAGCTAACCATTTTATTGCTTCAAC
*
21626734 CTGCTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTTGCTCGCA-TCA-AT-CG-TCGA
66 CTACTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTTGCTCGCATTCACATGCGTTCGA
* * * *
21626795 GTTGG-CATACTTCTCTGTATCTTATCAGGAAGATGACCGCCTC-TTTTTTTTCAATTCGTTTCT
131 GTTGGTC-TACTTCTCAGTATCTCATCAGGAAGATGACCGCCTCATTTGTTTT-AATTCGCTTCT
21626858 CTGGATCTCCTC
194 CTGGATCTCCTC
* *
21626870 AGGAAGACGAATTTGGTCCATTTCTCAGTGTCTCATCAGGAAGATAACCATTTTATTGCTTCAAC
1 AGGAAGACGAATTTGGTCCACTTCTCAGTGTCTCATCAGGAAGCTAACCATTTTATTGCTTCAAC
* * * * * *
21626935 CTACTTTTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCGCATTGAGCCTGGGTTTG
66 CTACTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTTGCTCGCATTCA-CATGCGTTCG
* * *
21627000 ATTTGGTCTTCTTCTCAGTGTCTCATCAGGAAGATGACCGCCTCATTTGTTTTAATTCGCTTCTC
130 AGTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCCTCATTTGTTTTAATTCGCTTCTC
21627065 TGGATCTCCTC
195 TGGATCTCCTC
21627076 AGGAAGAC-AATTTGGTCCACTTCTCAGTGTCTCATCAGGAAGCTAACCATTTTATTGCTTCAA
1 AGGAAGACGAATTTGGTCCACTTCTCAGTGTCTCATCAGGAAGCTAACCATTTTATTGCTTCAA
21627139 AATTTAATTT
Statistics
Matches: 238, Mismatches: 24, Indels: 10
0.88 0.09 0.04
Matches are distributed among these distances:
201 104 0.44
202 2 0.01
204 1 0.00
205 54 0.23
206 69 0.29
207 8 0.03
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (205 bp):
AGGAAGACGAATTTGGTCCACTTCTCAGTGTCTCATCAGGAAGCTAACCATTTTATTGCTTCAAC
CTACTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTTGCTCGCATTCACATGCGTTCGA
GTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCCTCATTTGTTTTAATTCGCTTCTCT
GGATCTCCTC
Found at i:21627078 original size:903 final size:903
Alignment explanation
Indices: 21625332--21628042 Score: 5235
Period size: 903 Copynumber: 3.0 Consensus size: 903
21625322 ATTTTAAAAT
21625332 AAATTTAATTTTAAAACAAATTCAAAATGGTTTGGTTGGCCCGGTCAAAATTGGGCTTCAACAGC
1 AAATTTAATTTTAAAACAAATTCAAAATGGTTTGGTTGGCCCGGTCAAAATTGGGCTTCAACAGC
21625397 TACCCCTCTTTGCTCGTTGTTGTGTAACAGGAACGGGGCAAAGACCAGAGGAAGACCAATTTTGC
66 TACCCCTCTTTGCTCGTTGTTGTGTAACAGGAACGGGGCAAAGACCAGAGGAAGACCAATTTTGC
21625462 CCAATTTACCAGGTTTCCTCCCTTTGATGCTCTTCTTTCGACTAGTTCGCCTTCGTTTTATTGAT
131 CCAATTTACCAGGTTTCCTCCCTTTGATGCTCTTCTTTCGACTAGTTCGCCTTCGTTTTATTGAT
*
21625527 CATTCGATTTTGCCGCATCCACCTTTCTATTTTTTCGATGTGGTGGTTCCATCCTGCTTTAGGGT
196 CATTCGATTTTGCCGCATCCACCTTTCTATTTTCTCGATGTGGTGGTTCCATCCTGCTTTAGGGT
21625592 AATCTTCAAAAAGTCAAAATTTGCTACTGTAATTTCCCTCCATTCTCTTGAAATTTCAAGGAGAT
261 AATCTTCAAAAAGTCAAAATTTGCTACTGTAATTTCCCTCCATTCTCTTGAAATTTCAAGGAGAT
21625657 TGGAATTCGTCACCGTAGTCTTTGGTTTTGTTGACTTGGCCCCATTCTCAGTGTCTCATCAGGAA
326 TGGAATTCGTCACCGTAGTCTTTGGTTTTGTTGACTTGGCCCC-TTCTCAGTGTCTCATCAGGAA
21625722 GGTGACTGCATCGTTTGTTTTGATCCACTTCTCTGTGTTTCAATAGGAAGACGGATTTGGTTCAC
390 GGTGACTGCATCGTTTGTTTTGATCCACTTCTCTGTGTTTCAATAGGAAGACGGATTTGGTTCAC
21625787 TTCTCTGTGGCTCATCAGAAAGCTAACCATTTTATTGCTTCTACCTGCTTCTCAGTATCTCATCA
455 TTCTCTGTGGCTCATCAGAAAGCTAACCATTTTATTGCTTCTACCTGCTTCTCAGTATCTCATCA
21625852 GGAAGCTGGGGTTCGAAGATTTGCTCGCATCAATCGTCGAGTTGGCATACTTCTCTGTATCTTAT
520 GGAAGCTGGGGTTCGAAGATTTGCTCGCATCAATCGTCGAGTTGGCATACTTCTCTGTATCTTAT
21625917 CAAGAAGATGACCGCCTCTTTTTTTTCAATTCGTTTCTCTGGATCTCTTCAGGAAGACGAATTTG
585 CAAGAAGATGACCGCCTCTTTTTTTTCAATTCGTTTCTCTGGATCTCTTCAGGAAGACGAATTTG
21625982 GTCCACTTCTCAGTGTCTCATCAGGAAGATAACCATTTTATTGCTTCAACCTGCTTCTCAGTATC
650 GTCCACTTCTCAGTGTCTCATCAGGAAGATAACCATTTTATTGCTTCAACCTGCTTCTCAGTATC
21626047 TCATCAGGAAGCTGGGGTTCGAAGATTTGCTCGCATTGAGCCTGGGTTTGATTTGGTCTTCTTCT
715 TCATCAGGAAGCTGGGGTTCGAAGATTTGCTCGCATTGAGCCTGGGTTTGATTTGGTCTTCTTCT
*
21626112 CTGTGTCTCATCAGGAAGATGACCGCCTCATTTGTTTTAATTCGCTTCTCTGGATCTCCTCAGGA
780 CAGTGTCTCATCAGGAAGATGACCGCCTCATTTGTTTTAATTCGCTTCTCTGGATCTCCTCAGGA
*
21626177 AGACGAATTTGGTCCACTTCTCAGTGTCTTATCAGGAAGCTAACCATTTTATTGCTTCG
845 AGACGAATTTGGTCCACTTCTCAGTGTCTCATCAGGAAGCTAACCATTTTATTGCTTCG
21626236 AAATTTAATTTTAAAACAAATTCAAAATGGTTTGGTTGGCCCGGTCAAAATTGGGCTTCAACAGC
1 AAATTTAATTTTAAAACAAATTCAAAATGGTTTGGTTGGCCCGGTCAAAATTGGGCTTCAACAGC
21626301 TACCCCTCTTTGCTCGTTGTTGTGTAACAGGAACGGGGCAAAGACCAGAGGAAGACCAATTTTGC
66 TACCCCTCTTTGCTCGTTGTTGTGTAACAGGAACGGGGCAAAGACCAGAGGAAGACCAATTTTGC
21626366 CCAATTTACCAGGTTTCCTCCCTTTGATGCTCTTCTTTCGACTAGTTCGCCTTCGTTTTATTGAT
131 CCAATTTACCAGGTTTCCTCCCTTTGATGCTCTTCTTTCGACTAGTTCGCCTTCGTTTTATTGAT
*
21626431 CATTCGATTTTGCCGCATCCACCTTTCTATTTTCTCGATGTGGTGGTTCCATCTTGCTTTAGGGT
196 CATTCGATTTTGCCGCATCCACCTTTCTATTTTCTCGATGTGGTGGTTCCATCCTGCTTTAGGGT
21626496 AATCTTCAAAAAGTCAAAATTTGCTACTGTAATTTCCCTCCATTCTCTTGAAATTTCAAGGAGAT
261 AATCTTCAAAAAGTCAAAATTTGCTACTGTAATTTCCCTCCATTCTCTTGAAATTTCAAGGAGAT
* * *
21626561 TGGATTTCGTCACCGTAGTCTTTGGTTTTGTTGACTTGGCCCCTTTTCAGTGTTTCATCAGGAAG
326 TGGAATTCGTCACCGTAGTCTTTGGTTTTGTTGACTTGGCCCCTTCTCAGTGTCTCATCAGGAAG
21626626 GTGACTGCATCGTTTGTTTTGATCCACTTCTCTGTGTTTCAATAGGAAGACGGATTTGGTTCACT
391 GTGACTGCATCGTTTGTTTTGATCCACTTCTCTGTGTTTCAATAGGAAGACGGATTTGGTTCACT
21626691 TCTCTGTGGCTCATCAGAAAGCTAACCATTTTATTGCTTCTACCTGCTTCTCAGTATCTCATCAG
456 TCTCTGTGGCTCATCAGAAAGCTAACCATTTTATTGCTTCTACCTGCTTCTCAGTATCTCATCAG
*
21626756 GAAGCTAGGGTTCGAAGATTTGCTCGCATCAATCGTCGAGTTGGCATACTTCTCTGTATCTTATC
521 GAAGCTGGGGTTCGAAGATTTGCTCGCATCAATCGTCGAGTTGGCATACTTCTCTGTATCTTATC
* *
21626821 AGGAAGATGACCGCCTCTTTTTTTTCAATTCGTTTCTCTGGATCTCCTCAGGAAGACGAATTTGG
586 AAGAAGATGACCGCCTCTTTTTTTTCAATTCGTTTCTCTGGATCTCTTCAGGAAGACGAATTTGG
* * *
21626886 TCCATTTCTCAGTGTCTCATCAGGAAGATAACCATTTTATTGCTTCAACCTACTTTTCAGTATCT
651 TCCACTTCTCAGTGTCTCATCAGGAAGATAACCATTTTATTGCTTCAACCTGCTTCTCAGTATCT
21626951 CATCAGGAAGCTGGGGTTCGAAGATTTGCTCGCATTGAGCCTGGGTTTGATTTGGTCTTCTTCTC
716 CATCAGGAAGCTGGGGTTCGAAGATTTGCTCGCATTGAGCCTGGGTTTGATTTGGTCTTCTTCTC
21627016 AGTGTCTCATCAGGAAGATGACCGCCTCATTTGTTTTAATTCGCTTCTCTGGATCTCCTCAGGAA
781 AGTGTCTCATCAGGAAGATGACCGCCTCATTTGTTTTAATTCGCTTCTCTGGATCTCCTCAGGAA
*
21627081 GAC-AATTTGGTCCACTTCTCAGTGTCTCATCAGGAAGCTAACCATTTTATTGCTTCA
846 GACGAATTTGGTCCACTTCTCAGTGTCTCATCAGGAAGCTAACCATTTTATTGCTTCG
*
21627138 AAATTTAATTTTAAAACAAATTCAAAATGGTTTGGTTGGCCCGGTCAAAATTAGGCTTCAACAGC
1 AAATTTAATTTTAAAACAAATTCAAAATGGTTTGGTTGGCCCGGTCAAAATTGGGCTTCAACAGC
21627203 TACCCCTCTTTGCTCGTTGTTGTGTAACAGGAACGGGGCAAAGACCAGAGGAAGACCAATTTTGC
66 TACCCCTCTTTGCTCGTTGTTGTGTAACAGGAACGGGGCAAAGACCAGAGGAAGACCAATTTTGC
21627268 CCAATTTACCAGGTTTCCTCCCTTTGATGCTCTTCTTTCGACTAGTTCGCCTTCGTTTTATTGAT
131 CCAATTTACCAGGTTTCCTCCCTTTGATGCTCTTCTTTCGACTAGTTCGCCTTCGTTTTATTGAT
21627333 CATTCGATTTTGCCGCATCCACCTTTCTATTTTCTCGATGTGGTGGTTCCATCCTGCTTTAGGGT
196 CATTCGATTTTGCCGCATCCACCTTTCTATTTTCTCGATGTGGTGGTTCCATCCTGCTTTAGGGT
*
21627398 AATCTTCAAAAAGTCAAAATTTACTACTGTAATTTCCCTCCATTCTCTTGAAATTTCAAGGAGAT
261 AATCTTCAAAAAGTCAAAATTTGCTACTGTAATTTCCCTCCATTCTCTTGAAATTTCAAGGAGAT
21627463 TGGAATTCGTCACCGTAGTCTTTGGTTTTGTTGACTTGGCCCCCTTCTCAGTGTCTCATCAGGAA
326 TGGAATTCGTCACCGTAGTCTTTGGTTTTGTTGACTTGG-CCCCTTCTCAGTGTCTCATCAGGAA
21627528 GGTGACTGCATCGTTTGTTTTGATCCACTTCTCTGTGTTTCAATAGGAAGACGGATTTGGTTCAC
390 GGTGACTGCATCGTTTGTTTTGATCCACTTCTCTGTGTTTCAATAGGAAGACGGATTTGGTTCAC
21627593 TTCTCTGTGGCTCATCAGAAAGCTAACCATTTTATTGCTTCTACCTGCTTCTCAGTATCTCATCA
455 TTCTCTGTGGCTCATCAGAAAGCTAACCATTTTATTGCTTCTACCTGCTTCTCAGTATCTCATCA
21627658 GGAAGCTGGGGTTCGAAGATTTGCTCGCATCAATCGTCGAGTTGGCATACTTCTCTGTATCTTAT
520 GGAAGCTGGGGTTCGAAGATTTGCTCGCATCAATCGTCGAGTTGGCATACTTCTCTGTATCTTAT
21627723 CAAGAAGATGACCGCCTCTTTTTTTTCAATTCGTTTCTCTGGATCTCTTCAGGAAGACGAATTTG
585 CAAGAAGATGACCGCCTCTTTTTTTTCAATTCGTTTCTCTGGATCTCTTCAGGAAGACGAATTTG
*
21627788 GTCCACTTCTCAGTGTCTCATTAGGAAGATAACCATTTTATTGCTTCAACCTGCTTCTCAGTATC
650 GTCCACTTCTCAGTGTCTCATCAGGAAGATAACCATTTTATTGCTTCAACCTGCTTCTCAGTATC
*
21627853 TCATCAGAAAGCTGGGGTTCGAAGATTTGCTCGCATTGAGCCTGGGTTTGATTTGGTCTTCTTCT
715 TCATCAGGAAGCTGGGGTTCGAAGATTTGCTCGCATTGAGCCTGGGTTTGATTTGGTCTTCTTCT
21627918 CAGTGTCTCATCAGGAAGATGACCGCCTCATTTGTTTTAATTCGCTTCTCTGGATCTCCTCAGGA
780 CAGTGTCTCATCAGGAAGATGACCGCCTCATTTGTTTTAATTCGCTTCTCTGGATCTCCTCAGGA
21627983 AGACGAATTTGGTCCACTTCTCAGTGTCTCATCAGGAAGCTAACCATTTTATTGCTTCG
845 AGACGAATTTGGTCCACTTCTCAGTGTCTCATCAGGAAGCTAACCATTTTATTGCTTCG
21628042 A
1 A
21628043 CCTGCTTCTC
Statistics
Matches: 1776, Mismatches: 29, Indels: 4
0.98 0.02 0.00
Matches are distributed among these distances:
902 412 0.23
903 945 0.53
904 419 0.24
ACGTcount: A:0.22, C:0.23, G:0.19, T:0.36
Consensus pattern (903 bp):
AAATTTAATTTTAAAACAAATTCAAAATGGTTTGGTTGGCCCGGTCAAAATTGGGCTTCAACAGC
TACCCCTCTTTGCTCGTTGTTGTGTAACAGGAACGGGGCAAAGACCAGAGGAAGACCAATTTTGC
CCAATTTACCAGGTTTCCTCCCTTTGATGCTCTTCTTTCGACTAGTTCGCCTTCGTTTTATTGAT
CATTCGATTTTGCCGCATCCACCTTTCTATTTTCTCGATGTGGTGGTTCCATCCTGCTTTAGGGT
AATCTTCAAAAAGTCAAAATTTGCTACTGTAATTTCCCTCCATTCTCTTGAAATTTCAAGGAGAT
TGGAATTCGTCACCGTAGTCTTTGGTTTTGTTGACTTGGCCCCTTCTCAGTGTCTCATCAGGAAG
GTGACTGCATCGTTTGTTTTGATCCACTTCTCTGTGTTTCAATAGGAAGACGGATTTGGTTCACT
TCTCTGTGGCTCATCAGAAAGCTAACCATTTTATTGCTTCTACCTGCTTCTCAGTATCTCATCAG
GAAGCTGGGGTTCGAAGATTTGCTCGCATCAATCGTCGAGTTGGCATACTTCTCTGTATCTTATC
AAGAAGATGACCGCCTCTTTTTTTTCAATTCGTTTCTCTGGATCTCTTCAGGAAGACGAATTTGG
TCCACTTCTCAGTGTCTCATCAGGAAGATAACCATTTTATTGCTTCAACCTGCTTCTCAGTATCT
CATCAGGAAGCTGGGGTTCGAAGATTTGCTCGCATTGAGCCTGGGTTTGATTTGGTCTTCTTCTC
AGTGTCTCATCAGGAAGATGACCGCCTCATTTGTTTTAATTCGCTTCTCTGGATCTCCTCAGGAA
GACGAATTTGGTCCACTTCTCAGTGTCTCATCAGGAAGCTAACCATTTTATTGCTTCG
Found at i:21628029 original size:206 final size:202
Alignment explanation
Indices: 21627506--21628148 Score: 796
Period size: 201 Copynumber: 3.2 Consensus size: 202
21627496 ACTTGGCCCC
* * * * * * * * *
21627506 CTTCTCAGTGTCTCATCAGGAAGGTGACTGCATCGTTTGTTTTGATCCACTTCTCTGTG-TTTCA
1 CTTCTCAGTATCTCATCAGGAAGATGACCGCCTCATTTGTTTTAATTCGCTTCTCTG-GATCTC-
* * * * *
21627570 AT-AGGAAGACGGATTTGGTTCACTTCTCTGTGGCTCATCAGAAAGCTAACCATTTTATTGCTTC
64 ATCAGGAAGACGAATTTGGTCCACTTCTCAGTGTCTCATCAGGAAGCTAACCATTTTATTGCTTC
* * ** * *
21627634 TACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCGCATCAATC-GTCGA
129 AACCTGCTTCTCAGTATCTCATCAGAAAGCTGGGGTTCGAAGATTTGCTCGCATTGAGCTGTTGA
21627698 GTTGG-CATA
194 GTTGGTC-TA
* * * * * *
21627707 CTTCTCTGTATCTTATCAAGAAGATGACCGCCTC-TTTTTTTTCAATTCGTTTCTCTGGATCTCT
1 CTTCTCAGTATCTCATCAGGAAGATGACCGCCTCATTTGTTTT-AATTCGCTTCTCTGGATCTCA
* *
21627771 TCAGGAAGACGAATTTGGTCCACTTCTCAGTGTCTCATTAGGAAGATAACCATTTTATTGCTTCA
65 TCAGGAAGACGAATTTGGTCCACTTCTCAGTGTCTCATCAGGAAGCTAACCATTTTATTGCTTCA
21627836 ACCTGCTTCTCAGTATCTCATCAGAAAGCTGGGGTTCGAAGATTTGCTCGCATTGAGCCTGGGTT
130 ACCTGCTTCTCAGTATCTCATCAGAAAGCTGGGGTTCGAAGATTTGCTCGCATTGAG-CT--G-T
* *
21627901 TGATTTGGTCTT
191 TGAGTTGGTCTA
* *
21627913 CTTCTCAGTGTCTCATCAGGAAGATGACCGCCTCATTTGTTTTAATTCGCTTCTCTGGATCTCCT
1 CTTCTCAGTATCTCATCAGGAAGATGACCGCCTCATTTGTTTTAATTCGCTTCTCTGGATCTCAT
*
21627978 CAGGAAGACGAATTTGGTCCACTTCTCAGTGTCTCATCAGGAAGCTAACCATTTTATTGCTTCGA
66 CAGGAAGACGAATTTGGTCCACTTCTCAGTGTCTCATCAGGAAGCTAACCATTTTATTGCTTCAA
* * * *
21628043 CCTGCTTCTCAGTGTCTCATCA-AGAAGTTGGGGTTCGAAGATTTGCCCGTATTGAGC-GTTGAG
131 CCTGCTTCTCAGTATCTCATCAGA-AAGCTGGGGTTCGAAGATTTGCTCGCATTGAGCTGTTGAG
*
21628106 TTGGTATA
195 TTGGTCTA
* *
21628114 CTTCTCTGTATCTCATCAGGAAGACGACCGCCTCA
1 CTTCTCAGTATCTCATCAGGAAGATGACCGCCTCA
21628149 ATGTTTTGTA
Statistics
Matches: 382, Mismatches: 49, Indels: 22
0.84 0.11 0.05
Matches are distributed among these distances:
200 9 0.02
201 190 0.50
202 2 0.01
205 3 0.01
206 170 0.45
207 8 0.02
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.35
Consensus pattern (202 bp):
CTTCTCAGTATCTCATCAGGAAGATGACCGCCTCATTTGTTTTAATTCGCTTCTCTGGATCTCAT
CAGGAAGACGAATTTGGTCCACTTCTCAGTGTCTCATCAGGAAGCTAACCATTTTATTGCTTCAA
CCTGCTTCTCAGTATCTCATCAGAAAGCTGGGGTTCGAAGATTTGCTCGCATTGAGCTGTTGAGT
TGGTCTA
Found at i:21628806 original size:100 final size:100
Alignment explanation
Indices: 21628639--21629388 Score: 1020
Period size: 100 Copynumber: 7.5 Consensus size: 100
21628629 AAATCTTCGT
* * * * * * *
21628639 GGTATTGGATCCGCCATTGC-GTCTTAGATCTTTTCCTTCCTATTTCTGAGGTGCACGGTCCACC
1 GGTACTGGATCCGCCATTGCGGTCTTAGATCTTTCCCGTCATGTTTCTGAGGTACACGGTCCGCC
21628703 GTTGCGACTTAGACCTTTCCCTTTAGTATCTTTGC
66 GTTGCGACTTAGACCTTTCCCTTTAGTATCTTTGC
* * * *
21628738 GGTACTAGATCCGCCATTGCGGTCTTAGATCTTTCCCGTCGTGTTTTTGAGGTACACGGTCCGTC
1 GGTACTGGATCCGCCATTGCGGTCTTAGATCTTTCCCGTCATGTTTCTGAGGTACACGGTCCGCC
*
21628803 GTTGCAACTTAGACCTTTCCCTTTAGTATCTTTGC
66 GTTGCGACTTAGACCTTTCCCTTTAGTATCTTTGC
* * * * *
21628838 GATACTGGATCCGCCATTACGGTCTTAGATCTTTCCCGTCGTGTTTTTAAGGTACACGGTCCGCC
1 GGTACTGGATCCGCCATTGCGGTCTTAGATCTTTCCCGTCATGTTTCTGAGGTACACGGTCCGCC
* *
21628903 GTTACTACTTAGACCTTTCCCTTTAGTATCTTTGC
66 GTTGCGACTTAGACCTTTCCCTTTAGTATCTTTGC
* * * ** * *
21628938 GGTACTGGATCCGTCATTGCGTTCTTAAATCTTTCCCGTTGTGTTTCTGAGGTATACGGTCTGCC
1 GGTACTGGATCCGCCATTGCGGTCTTAGATCTTTCCCGTCATGTTTCTGAGGTACACGGTCCGCC
*
21629003 GTTGCGACTTAGACCTTTCCCTTTAGTATATTTGC
66 GTTGCGACTTAGACCTTTCCCTTTAGTATCTTTGC
* * * * *
21629038 AGTACTGGATCCGCCATTGAGGTCTTAGATCTTTCCCGTCATGTTTTTAAGGTACACGATCCGCC
1 GGTACTGGATCCGCCATTGCGGTCTTAGATCTTTCCCGTCATGTTTCTGAGGTACACGGTCCGCC
21629103 GTTGCGACTTAGACCTTTCCCTTTAGTATCTTTGC
66 GTTGCGACTTAGACCTTTCCCTTTAGTATCTTTGC
* * *
21629138 GGTACTGGATCCGCCATTACGGTCTTAGATCGTTCCCGTCATGTTTCTGAGGTACACGGTCCGTC
1 GGTACTGGATCCGCCATTGCGGTCTTAGATCTTTCCCGTCATGTTTCTGAGGTACACGGTCCGCC
* *
21629203 GTTGCGACTTAGATCTTTCCCTTTTGTATCTTTGC
66 GTTGCGACTTAGACCTTTCCCTTTAGTATCTTTGC
* * *
21629238 GGTACTGGAT-CGCCATTGCGGTCTTAGATCTTTCCCTTTCATGCTTCTGAGGTACACGGTCTGC
1 GGTACTGGATCCGCCATTGCGGTCTTAGATCTTTCCC-GTCATGTTTCTGAGGTACACGGTCCGC
* * * *
21629302 CGTTACGACTTAGACCTTTCCCTGTT-GTGTTTTTAC
65 CGTTGCGACTTAGACCTTTCCCT-TTAGTATCTTTGC
* * * *
21629338 GGTACTGGATCTGCAATTGCAGTCTTAGATCTTTCCCTTTCATGTTTCTGA
1 GGTACTGGATCCGCCATTGCGGTCTTAGATCTTTCCC-GTCATGTTTCTGA
21629389 TGCTGAAACC
Statistics
Matches: 578, Mismatches: 69, Indels: 6
0.89 0.11 0.01
Matches are distributed among these distances:
99 42 0.07
100 498 0.86
101 38 0.07
ACGTcount: A:0.15, C:0.26, G:0.21, T:0.38
Consensus pattern (100 bp):
GGTACTGGATCCGCCATTGCGGTCTTAGATCTTTCCCGTCATGTTTCTGAGGTACACGGTCCGCC
GTTGCGACTTAGACCTTTCCCTTTAGTATCTTTGC
Found at i:21630627 original size:16 final size:16
Alignment explanation
Indices: 21630606--21630642 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
21630596 TCTCCTTTTC
21630606 TTTTTTTTCTTGTTTG
1 TTTTTTTTCTTGTTTG
* *
21630622 TTTTTTTTGTTTTTTG
1 TTTTTTTTCTTGTTTG
21630638 TTTTT
1 TTTTT
21630643 GTTTTTCTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.00, C:0.03, G:0.11, T:0.86
Consensus pattern (16 bp):
TTTTTTTTCTTGTTTG
Found at i:21630631 original size:13 final size:12
Alignment explanation
Indices: 21630601--21630648 Score: 60
Period size: 13 Copynumber: 3.8 Consensus size: 12
21630591 CGTCCTCTCC
*
21630601 TTTTCTTTTTTT
1 TTTTGTTTTTTT
*
21630613 TCTTGTTTGTTTT
1 TTTTGTTT-TTTT
21630626 TTTTGTTTTTTGT
1 TTTTGTTTTTT-T
21630639 TTTTGTTTTT
1 TTTTGTTTTT
21630649 CTTCTTCTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
12 9 0.29
13 22 0.71
ACGTcount: A:0.00, C:0.04, G:0.10, T:0.85
Consensus pattern (12 bp):
TTTTGTTTTTTT
Found at i:21636538 original size:11 final size:11
Alignment explanation
Indices: 21636522--21636547 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
21636512 TTTAATATGG
21636522 ATGAGCAATTA
1 ATGAGCAATTA
21636533 ATGAGCAATTA
1 ATGAGCAATTA
21636544 ATGA
1 ATGA
21636548 TGGATATTAA
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:0.46, C:0.08, G:0.19, T:0.27
Consensus pattern (11 bp):
ATGAGCAATTA
Found at i:21636802 original size:57 final size:56
Alignment explanation
Indices: 21636697--21636866 Score: 195
Period size: 57 Copynumber: 3.0 Consensus size: 56
21636687 TTTGGATACC
*
21636697 CGAGGGTAAAATGGTAA-TTTTGGTTGAAATTGGGTCAAAAT-AGGATTTTAGAAAGTT
1 CGAGGG-AAAATGGTAATTTTTGG-TAAAATTGGGTCAAAATGA-GATTTTAGAAAGTT
* *
21636754 CGGGGGAAAATGGTAATTTTTGGTAAAATTGGAGTTAAAATGAGATTTTAGAAAGTT
1 CGAGGGAAAATGGTAATTTTTGGTAAAATTGG-GTCAAAATGAGATTTTAGAAAGTT
* * * *
21636811 CGAGGGAAAATGGCAATTTTT-GTAAAATCGGGGTGAAAATG-GAATTTTAAAAAGTT
1 CGAGGGAAAATGGTAATTTTTGGTAAAAT-TGGGTCAAAATGAG-ATTTTAGAAAGTT
21636867 TTGAGGTCAA
Statistics
Matches: 100, Mismatches: 8, Indels: 11
0.84 0.07 0.09
Matches are distributed among these distances:
55 1 0.01
56 45 0.45
57 53 0.53
58 1 0.01
ACGTcount: A:0.37, C:0.04, G:0.28, T:0.32
Consensus pattern (56 bp):
CGAGGGAAAATGGTAATTTTTGGTAAAATTGGGTCAAAATGAGATTTTAGAAAGTT
Found at i:21636822 original size:27 final size:26
Alignment explanation
Indices: 21636733--21636823 Score: 74
Period size: 27 Copynumber: 3.3 Consensus size: 26
21636723 AAATTGGGTC
*
21636733 AAAATAGGATTTTAGAAAGTTCGGGGG
1 AAAAT-GGATTTTAGAAAGTTCGAGGG
* * * **
21636760 AAAATGGTAATTTTTGGTAAAATTGGAGTT
1 AAAATGG--A-TTTTAG-AAAGTTCGAGGG
21636790 AAAATGAGATTTTAGAAAGTTCGAGGG
1 AAAATG-GATTTTAGAAAGTTCGAGGG
21636817 AAAATGG
1 AAAATGG
21636824 CAATTTTTGT
Statistics
Matches: 48, Mismatches: 11, Indels: 11
0.69 0.16 0.16
Matches are distributed among these distances:
26 3 0.06
27 19 0.40
28 6 0.12
29 6 0.12
30 13 0.27
31 1 0.02
ACGTcount: A:0.40, C:0.02, G:0.29, T:0.30
Consensus pattern (26 bp):
AAAATGGATTTTAGAAAGTTCGAGGG
Found at i:21636926 original size:30 final size:29
Alignment explanation
Indices: 21636853--21637027 Score: 174
Period size: 30 Copynumber: 5.9 Consensus size: 29
21636843 GTGAAAATGG
* * * *
21636853 AATTTTAAAAAGTTTTGAGGTCAAAATAT
1 AATTTTAGAAAGTTTAGGGGTTAAAATAT
21636882 AA-TTTAGAAAAGTTTAGGGGTTAAAATAT
1 AATTTTAG-AAAGTTTAGGGGTTAAAATAT
* *
21636911 AATTTATAGAAAGTTTTA-AGGTCAAAATAT
1 AATTT-TAGAAAG-TTTAGGGGTTAAAATAT
* * *
21636941 AATTTTGGAAAATTTAGGGGTTAAAATGT
1 AATTTTAGAAAGTTTAGGGGTTAAAATAT
* * *
21636970 AATTTACAAAAAGTTTTGGGGTTAAAATAT
1 AATTT-TAGAAAGTTTAGGGGTTAAAATAT
*
21637000 AATTTTAGAATAGTTCAGGGGTTAAAAT
1 AATTTTAGAA-AGTTTAGGGGTTAAAAT
21637028 GCCATTTTTG
Statistics
Matches: 118, Mismatches: 21, Indels: 13
0.78 0.14 0.09
Matches are distributed among these distances:
28 8 0.07
29 44 0.37
30 59 0.50
31 7 0.06
ACGTcount: A:0.43, C:0.02, G:0.18, T:0.37
Consensus pattern (29 bp):
AATTTTAGAAAGTTTAGGGGTTAAAATAT
Found at i:21636937 original size:59 final size:60
Alignment explanation
Indices: 21636853--21637027 Score: 248
Period size: 59 Copynumber: 3.0 Consensus size: 60
21636843 GTGAAAATGG
21636853 AATTT-TAAAAAGTTTTGAGGTCAAAATATAA-TTTAGAAAAGTTTAGGGGTTAAAATAT
1 AATTTATAAAAAGTTTTGAGGTCAAAATATAATTTTAGAAAAGTTTAGGGGTTAAAATAT
* * * *
21636911 AATTTATAGAAAGTTTTAAGGTCAAAATATAATTTTGGAAAA-TTTAGGGGTTAAAATGT
1 AATTTATAAAAAGTTTTGAGGTCAAAATATAATTTTAGAAAAGTTTAGGGGTTAAAATAT
* * * * *
21636970 AATTTACAAAAAGTTTTGGGGTTAAAATATAATTTTAGAATAGTTCAGGGGTTAAAAT
1 AATTTATAAAAAGTTTTGAGGTCAAAATATAATTTTAGAAAAGTTTAGGGGTTAAAAT
21637028 GCCATTTTTG
Statistics
Matches: 102, Mismatches: 12, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
58 5 0.05
59 75 0.74
60 22 0.22
ACGTcount: A:0.43, C:0.02, G:0.18, T:0.37
Consensus pattern (60 bp):
AATTTATAAAAAGTTTTGAGGTCAAAATATAATTTTAGAAAAGTTTAGGGGTTAAAATAT
Found at i:21637035 original size:30 final size:30
Alignment explanation
Indices: 21636875--21637050 Score: 83
Period size: 30 Copynumber: 5.9 Consensus size: 30
21636865 TTTTGAGGTC
* * *
21636875 AAAATATAA-TTTAGAAAAGTTTAGGGGTT
1 AAAATACAATTTTAGAATAGTTCAGGGGTT
* * * *
21636904 AAAATATAATTTATAGAA-AGTTTTA-AGGTC
1 AAAATACAATTT-TAGAATAG-TTCAGGGGTT
* * * *
21636934 AAAATATAATTTTGGAA-AATTTAGGGGTT
1 AAAATACAATTTTAGAATAGTTCAGGGGTT
** * * **
21636963 AAAATGTAA-TTTACAAAAAGTTTTGGGGTT
1 AAAATACAATTTTA-GAATAGTTCAGGGGTT
*
21636993 AAAATATAATTTTAGAATAGTTCAGGGGTT
1 AAAATACAATTTTAGAATAGTTCAGGGGTT
* * * * *
21637023 AAAATGCCATTTTTGGATAGTTTAGGGG
1 AAAATACAATTTTAGAATAGTTCAGGGG
21637051 CTTTTAGAGC
Statistics
Matches: 118, Mismatches: 22, Indels: 13
0.77 0.14 0.08
Matches are distributed among these distances:
28 7 0.06
29 27 0.23
30 71 0.60
31 13 0.11
ACGTcount: A:0.40, C:0.03, G:0.20, T:0.36
Consensus pattern (30 bp):
AAAATACAATTTTAGAATAGTTCAGGGGTT
Found at i:21638001 original size:22 final size:23
Alignment explanation
Indices: 21637964--21638028 Score: 73
Period size: 23 Copynumber: 2.9 Consensus size: 23
21637954 TTTTAGTTTC
*
21637964 TTTTTATT-ATATTATTACTA-A
1 TTTTTATTAATATTATTAATATA
*
21637985 TTTTTATTAATGA-TATTAATATT
1 TTTTTATTAAT-ATTATTAATATA
21638008 TTTTTATTAATACTTATTAAT
1 TTTTTATTAATA-TTATTAAT
21638029 GCTATTTACT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
21 8 0.22
22 10 0.27
23 12 0.32
24 7 0.19
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.62
Consensus pattern (23 bp):
TTTTTATTAATATTATTAATATA
Done.