Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004388.1 Hibiscus syriacus cultivar Beakdansim tig00009620_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 75460
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:6233 original size:31 final size:30
Alignment explanation
Indices: 6195--6298 Score: 127
Period size: 31 Copynumber: 3.4 Consensus size: 30
6185 AACTCAAAAC
* * * *
6195 TTTGTGACGGAACATGTGGACCCGTCAGAAA
1 TTTGTGACGGAA-AAGTGAATCTGTCAGAAA
*
6226 TTTGTGACGGAAAAGGTGAATATGTCAGAAA
1 TTTGTGACGGAAAA-GTGAATCTGTCAGAAA
*
6257 TTTGTGACGGAATAGATGAATCTGTCAGAAA
1 TTTGTGACGGAAAAG-TGAATCTGTCAGAAA
6288 TTTGTGACGGA
1 TTTGTGACGGA
6299 CCCACATATT
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
30 2 0.03
31 62 0.97
ACGTcount: A:0.33, C:0.12, G:0.29, T:0.27
Consensus pattern (30 bp):
TTTGTGACGGAAAAGTGAATCTGTCAGAAA
Found at i:7635 original size:24 final size:24
Alignment explanation
Indices: 7603--7651 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
7593 AGTCTTCCTG
7603 ATGATGTATAAAACATCTATGTAC
1 ATGATGTATAAAACATCTATGTAC
*
7627 ATGATGTATAAAATATCTATGTAC
1 ATGATGTATAAAACATCTATGTAC
7651 A
1 A
7652 ATGTCATGCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.35
Consensus pattern (24 bp):
ATGATGTATAAAACATCTATGTAC
Found at i:8229 original size:31 final size:29
Alignment explanation
Indices: 8194--8257 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 29
8184 TATTCATAAC
* **
8194 TTTTCCAAAATTATTGAATTGGTCCCCTAAA
1 TTTTCAAAAATTAAAGAA-TGGTCCCC-AAA
8225 TTTTCAAAAATTAAAGAATGGTCCCCAAA
1 TTTTCAAAAATTAAAGAATGGTCCCCAAA
8254 TTTT
1 TTTT
8258 TATAAGGCTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 7 0.23
30 8 0.27
31 15 0.50
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.38
Consensus pattern (29 bp):
TTTTCAAAAATTAAAGAATGGTCCCCAAA
Found at i:9354 original size:27 final size:27
Alignment explanation
Indices: 9324--9408 Score: 75
Period size: 30 Copynumber: 3.0 Consensus size: 27
9314 GCCAATTTGT
9324 AACTTT-TAAATTACTATTTGGTCCCTA
1 AACTTTATAAATTA-TATTTGGTCCCTA
*
9351 AACTTTTCTAAAGTTATACTTTGGTCACC-A
1 AAC-TTTATAAA-TTATA-TTTGGTC-CCTA
* * *
9381 AACTTTAAAAATTTTATTTGGTCACTA
1 AACTTTATAAATTATATTTGGTCCCTA
9408 A
1 A
9409 CTAAATTCAT
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
26 1 0.02
27 12 0.25
28 7 0.15
29 12 0.25
30 14 0.29
31 2 0.04
ACGTcount: A:0.33, C:0.16, G:0.08, T:0.42
Consensus pattern (27 bp):
AACTTTATAAATTATATTTGGTCCCTA
Found at i:15654 original size:33 final size:30
Alignment explanation
Indices: 15599--15659 Score: 77
Period size: 33 Copynumber: 1.9 Consensus size: 30
15589 GAAGTGATTT
*
15599 AATAATTTTTTATTTATATTTTATGTTTTA
1 AATAATTTTTTATTTATATTTTAGGTTTTA
*
15629 AATAATTATTTTATTTTAATGTTTTAGGTTT
1 AATAATT-TTTTA-TTT-ATATTTTAGGTTT
15660 AGACCAAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 7 0.27
31 5 0.19
32 3 0.12
33 11 0.42
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.64
Consensus pattern (30 bp):
AATAATTTTTTATTTATATTTTAGGTTTTA
Found at i:16022 original size:2 final size:2
Alignment explanation
Indices: 16010--16053 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
16000 TTTATTAAAC
16010 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
16051 TA T
1 TA T
16054 GTTATTTTCA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:17951 original size:31 final size:31
Alignment explanation
Indices: 17890--17951 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 31
17880 GTACCTAGTA
*
17890 GGGTCAAATCGAGTCGATTGGTTTTCGGTTC
1 GGGTCAAATCGAGTCGATTGGTTTTAGGTTC
*
17921 GGGTCAATATCG-GATCGGTTGG-TTTAGGTTC
1 GGGTCAA-ATCGAG-TCGATTGGTTTTAGGTTC
17952 TGGTAAGGCT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
31 16 0.59
32 11 0.41
ACGTcount: A:0.16, C:0.15, G:0.34, T:0.35
Consensus pattern (31 bp):
GGGTCAAATCGAGTCGATTGGTTTTAGGTTC
Found at i:18073 original size:46 final size:46
Alignment explanation
Indices: 17960--18097 Score: 152
Period size: 46 Copynumber: 3.0 Consensus size: 46
17950 TCTGGTAAGG
* * ** *
17960 CTTTAGATTTTCAGGTCAATTTAGGTTGATTTCGGTTCGGATCAAC
1 CTTTAAATTTTCAAGTCAATTCGGGTTGGTTTCGGTTCGGATCAAC
*
18006 CTTTAAATTTTCAAGTCAATTCGGGTTGGTTTAGGTTCGGATCAAC
1 CTTTAAATTTTCAAGTCAATTCGGGTTGGTTTCGGTTCGGATCAAC
* ** * ** *
18052 CTTTAGATTTTTGAGTTAATTCGAATT-GTTTCGGTTTGGATCAAC
1 CTTTAAATTTTCAAGTCAATTCGGGTTGGTTTCGGTTCGGATCAAC
18097 C
1 C
18098 GTCGTCACCC
Statistics
Matches: 78, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
45 17 0.22
46 61 0.78
ACGTcount: A:0.22, C:0.14, G:0.21, T:0.42
Consensus pattern (46 bp):
CTTTAAATTTTCAAGTCAATTCGGGTTGGTTTCGGTTCGGATCAAC
Found at i:18413 original size:5 final size:5
Alignment explanation
Indices: 18403--18433 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
18393 AATATATATA
18403 TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT T
1 TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT T
18434 GTTTATATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TTAAT
Found at i:19811 original size:126 final size:126
Alignment explanation
Indices: 19657--19889 Score: 330
Period size: 126 Copynumber: 1.8 Consensus size: 126
19647 TCTTGGTTGG
* *
19657 TTCTTCATCAGATTGGGTAGGTGGTGGTTGCTTGT-GGAGCAAGGAACCTAAA-TCGGAACGA-G
1 TTCTTCATCAGATTGGGTAGGTGATGGTTGCTTGTCAG-GCAAGGAACCTAAATTC-GAA-GATG
* *
19719 G-TTTCTCACCCAATTTTCTAGCCGAACCCGTGAAAGGTTTGAACTCAGTTTTACCGGCCATTTT
63 GATTT-TCACCCAATTTTCTAGCCAAACCAGTGAAAGGTTTGAACTCAGTTTTACCGGCCATTTT
* * *
19783 TTCTTCATCAGATTGGGTAGTTGATGGTTGCTTGTCAGGCAAGGAGCCTAAATTCGAATATGGAT
1 TTCTTCATCAGATTGGGTAGGTGATGGTTGCTTGTCAGGCAAGGAACCTAAATTCGAAGATGGAT
*
19848 TTTCACCCAATTTTCTAGCTAAACCAGTGAAAGGTTTGAACT
66 TTTCACCCAATTTTCTAGCCAAACCAGTGAAAGGTTTGAACT
19890 TGGATTTCTC
Statistics
Matches: 95, Mismatches: 8, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
125 1 0.01
126 88 0.93
127 6 0.06
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (126 bp):
TTCTTCATCAGATTGGGTAGGTGATGGTTGCTTGTCAGGCAAGGAACCTAAATTCGAAGATGGAT
TTTCACCCAATTTTCTAGCCAAACCAGTGAAAGGTTTGAACTCAGTTTTACCGGCCATTTT
Found at i:21461 original size:2 final size:2
Alignment explanation
Indices: 21454--21486 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
21444 TTTTCATGTT
21454 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
21487 TAAAGTCTCT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:21526 original size:18 final size:19
Alignment explanation
Indices: 21505--21541 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
21495 CTTTTATTAG
*
21505 TTAAAAC-GAATTTAAATT
1 TTAAAACTGAAATTAAATT
21523 TTAAAACTGAAATTAAATT
1 TTAAAACTGAAATTAAATT
21542 GATATAACCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.38
Consensus pattern (19 bp):
TTAAAACTGAAATTAAATT
Found at i:22740 original size:20 final size:19
Alignment explanation
Indices: 22667--22739 Score: 128
Period size: 19 Copynumber: 3.8 Consensus size: 19
22657 AGTAGACTTT
22667 AGAGTTTCAAAACTTCACA
1 AGAGTTTCAAAACTTCACA
22686 AGAGTTTCAAAACTTCACA
1 AGAGTTTCAAAACTTCACA
*
22705 AGAGTTTCAAAACTTTAACA
1 AGAGTTTCAAAAC-TTCACA
22725 AGAGTTTCAAAACTT
1 AGAGTTTCAAAACTT
22740 TCCTTGTAGT
Statistics
Matches: 52, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
19 34 0.65
20 18 0.35
ACGTcount: A:0.42, C:0.18, G:0.11, T:0.29
Consensus pattern (19 bp):
AGAGTTTCAAAACTTCACA
Found at i:24505 original size:20 final size:22
Alignment explanation
Indices: 24480--24519 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
24470 TGTTGTATAT
24480 AGTCG-TTGGGGAT-ATTTTGG
1 AGTCGTTTGGGGATGATTTTGG
24500 AGTCGTTTGGGGATGATTTT
1 AGTCGTTTGGGGATGATTTT
24520 TCTGCAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 8 0.44
22 5 0.28
ACGTcount: A:0.15, C:0.05, G:0.38, T:0.42
Consensus pattern (22 bp):
AGTCGTTTGGGGATGATTTTGG
Found at i:25051 original size:21 final size:19
Alignment explanation
Indices: 25027--25084 Score: 82
Period size: 18 Copynumber: 3.0 Consensus size: 19
25017 ATGTTTAATG
*
25027 AAAAAGATACCAATTGTTA
1 AAAAAGATATCAATTGTTA
25046 ACAAAATGATATCAATTGTT-
1 A-AAAA-GATATCAATTGTTA
25066 AAAAAGATATCAATTGTTA
1 AAAAAGATATCAATTGTTA
25085 CCAATTGTTG
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
18 13 0.37
19 5 0.14
20 5 0.14
21 12 0.34
ACGTcount: A:0.50, C:0.09, G:0.10, T:0.31
Consensus pattern (19 bp):
AAAAAGATATCAATTGTTA
Found at i:27804 original size:34 final size:33
Alignment explanation
Indices: 27741--27811 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 33
27731 CCTTTACAAC
* *
27741 TCCCTAGTTTTTCATGGGATAACCTAGAACCTT
1 TCCCTAGTTTTACACGGGATAACCTAGAACCTT
* *
27774 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAG-TTTTACACGGGATAACCTAGAACCTT
27808 TCCC
1 TCCC
27812 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
33 7 0.21
34 26 0.79
ACGTcount: A:0.23, C:0.30, G:0.15, T:0.32
Consensus pattern (33 bp):
TCCCTAGTTTTACACGGGATAACCTAGAACCTT
Found at i:28190 original size:20 final size:20
Alignment explanation
Indices: 28165--28203 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
28155 CGTTGCAGCT
* *
28165 AGGGTGCATGGATGCACTGC
1 AGGGTGCATCGATACACTGC
28185 AGGGTGCATCGATACACTG
1 AGGGTGCATCGATACACTG
28204 TGCATTAGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.23, C:0.21, G:0.36, T:0.21
Consensus pattern (20 bp):
AGGGTGCATCGATACACTGC
Found at i:32767 original size:63 final size:65
Alignment explanation
Indices: 32690--32848 Score: 177
Period size: 64 Copynumber: 2.5 Consensus size: 65
32680 GAATTAAATT
* *
32690 GAACATCGAATGCATCCCATTCATCGATGCA-CA-CCATGCACCGATGCACT-GAGGAT-TTTAT
1 GAACATCGAATGCATCCCATGCATCGATGCACCAGCCATGCAACGATGCACTCG-GGATATTT-T
32751 AA
64 AA
*** *
32753 GAACATCGAATGCATTTGATGCATCGATGCACCAGCCATGCAACGATGCACTCGGGCTATTTTAA
1 GAACATCGAATGCATCCCATGCATCGATGCACCAGCCATGCAACGATGCACTCGGGATATTTTAA
**
32818 -AACATCGAATGCA-CTTGATGCATCGATGCAC
1 GAACATCGAATGCATC-CCATGCATCGATGCAC
32849 TCTAAGTGCA
Statistics
Matches: 84, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
63 27 0.32
64 31 0.37
65 22 0.26
66 4 0.05
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (65 bp):
GAACATCGAATGCATCCCATGCATCGATGCACCAGCCATGCAACGATGCACTCGGGATATTTTAA
Found at i:32836 original size:64 final size:64
Alignment explanation
Indices: 32711--32848 Score: 194
Period size: 64 Copynumber: 2.2 Consensus size: 64
32701 GCATCCCATT
* *
32711 CATCGATGCA-CACCATGCACCGATGCACTGAGGATTTTATAAGAACATCGAATGCATTTGATG
1 CATCGATGCACCACCATGCAACGATGCACTGAGGATTTTATAAGAACATCGAATGCACTTGATG
*
32774 CATCGATGCACCAGCCATGCAACGATGCACTCG-GGCTATTT-TAA-AACATCGAATGCACTTGA
1 CATCGATGCACCA-CCATGCAACGATGCACT-GAGGAT-TTTATAAGAACATCGAATGCACTTGA
32836 TG
63 TG
32838 CATCGATGCAC
1 CATCGATGCAC
32849 TCTAAGTGCA
Statistics
Matches: 68, Mismatches: 3, Indels: 7
0.87 0.04 0.09
Matches are distributed among these distances:
63 10 0.15
64 32 0.47
65 22 0.32
66 4 0.06
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.24
Consensus pattern (64 bp):
CATCGATGCACCACCATGCAACGATGCACTGAGGATTTTATAAGAACATCGAATGCACTTGATG
Found at i:32864 original size:64 final size:63
Alignment explanation
Indices: 32711--32868 Score: 173
Period size: 64 Copynumber: 2.5 Consensus size: 63
32701 GCATCCCATT
* *
32711 CATCGATGCA-CACCATGCACCGATGCACTGAGGATTTTATAAGAACATCGAATGCATTTGATG
1 CATCGATGCACCAGC-TGCACCGATGCACTGAGGATTTTATAAGAACATCGAATGCACTTGATG
* *
32774 CATCGATGCACCAGCCATGCAACGATGCACTCG-GGCTATTT-TAA-AACATCGAATGCACTTGA
1 CATCGATGCACCAG-C-TGCACCGATGCACT-GAGGAT-TTTATAAGAACATCGAATGCACTTGA
32836 TG
62 TG
32838 CATCGATGCACTCTAAG-TGCACCGATGCACT
1 CATCGATGCAC-C--AGCTGCACCGATGCACT
32869 AAGGTTCCAA
Statistics
Matches: 83, Mismatches: 5, Indels: 13
0.82 0.05 0.13
Matches are distributed among these distances:
63 10 0.12
64 45 0.54
65 22 0.27
66 4 0.05
67 2 0.02
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (63 bp):
CATCGATGCACCAGCTGCACCGATGCACTGAGGATTTTATAAGAACATCGAATGCACTTGATG
Found at i:40278 original size:21 final size:21
Alignment explanation
Indices: 40249--40292 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
40239 ACTCCGAGAG
* *
40249 CTAGTTCCTCTCGAGCTGCTC
1 CTAGCTCCTCTCGAGCTCCTC
*
40270 CTAGCTCCTCTCGTGCTCCTC
1 CTAGCTCCTCTCGAGCTCCTC
40291 CT
1 CT
40293 CCTCCTCCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.07, C:0.43, G:0.16, T:0.34
Consensus pattern (21 bp):
CTAGCTCCTCTCGAGCTCCTC
Found at i:41029 original size:19 final size:19
Alignment explanation
Indices: 40983--41020 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
40973 AAAGGGGGAG
40983 AAATGTTAAGTGTTGAAAT
1 AAATGTTAAGTGTTGAAAT
41002 AAATGTTAAGTGTTGAAAT
1 AAATGTTAAGTGTTGAAAT
41021 GATTTTTAAA
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:0.42, C:0.00, G:0.21, T:0.37
Consensus pattern (19 bp):
AAATGTTAAGTGTTGAAAT
Found at i:41455 original size:17 final size:17
Alignment explanation
Indices: 41442--41474 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
41432 TGAATGCATC
*
41442 CCATGCATCGATGCACA
1 CCATGCACCGATGCACA
41459 CCATGCACCGATGCAC
1 CCATGCACCGATGCAC
41475 TGAGGATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.39, G:0.18, T:0.15
Consensus pattern (17 bp):
CCATGCACCGATGCACA
Found at i:41572 original size:64 final size:64
Alignment explanation
Indices: 41444--41604 Score: 186
Period size: 64 Copynumber: 2.5 Consensus size: 64
41434 AATGCATCCC
* *
41444 ATGCATCGATGCA-CACCATGCACCGATGCACTGAGGATTTTATAAGAACATCGAATGCATTTG
1 ATGCATCGATGCACCACAATGCACCGATGCACTGAGGATTTTATAAGAACATCGAATGCACTTG
* * *
41507 ATGCATCGATGCACCAGCAATGCATCGATGCACTCG-GGCTATTT-TAA-AACATCGAATTCACT
1 ATGCATCGATGCACCA-CAATGCACCGATGCACT-GAGGAT-TTTATAAGAACATCGAATGCACT
41569 TG
63 TG
** *
41571 ATGCATCGATGCACTCTTAGTGCACCGATGCACT
1 ATGCATCGATGCAC-CACAATGCACCGATGCACT
41605 AAGGTTCCAA
Statistics
Matches: 84, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
63 13 0.15
64 45 0.54
65 22 0.26
66 4 0.05
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.26
Consensus pattern (64 bp):
ATGCATCGATGCACCACAATGCACCGATGCACTGAGGATTTTATAAGAACATCGAATGCACTTG
Found at i:43954 original size:2 final size:2
Alignment explanation
Indices: 43947--44016 Score: 140
Period size: 2 Copynumber: 35.0 Consensus size: 2
43937 TTACAAAAAT
43947 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
43989 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
44017 AAGAAACCAA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:47489 original size:16 final size:17
Alignment explanation
Indices: 47455--47487 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
47445 TTTCGGTTTG
*
47455 AAAAAATCCGGTTTTTT
1 AAAAAAACCGGTTTTTT
47472 AAAAAAACCGGTTTTT
1 AAAAAAACCGGTTTTT
47488 AATCTGGTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.36
Consensus pattern (17 bp):
AAAAAAACCGGTTTTTT
Found at i:54942 original size:6 final size:6
Alignment explanation
Indices: 54924--54954 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
54914 AGTTTAACTC
*
54924 TTTAAG TTAAAG TTTAAG TTTAAG TTTAAG T
1 TTTAAG TTTAAG TTTAAG TTTAAG TTTAAG T
54955 GAATTTTAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.16, T:0.48
Consensus pattern (6 bp):
TTTAAG
Found at i:55922 original size:12 final size:12
Alignment explanation
Indices: 55902--55936 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
55892 CCCAACTTGT
55902 AAAGTAGAAAAA
1 AAAGTAGAAAAA
* *
55914 AAAGGAGAAAGA
1 AAAGTAGAAAAA
55926 AAAGTAGAAAA
1 AAAGTAGAAAA
55937 CGGCTAGGAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.71, C:0.00, G:0.23, T:0.06
Consensus pattern (12 bp):
AAAGTAGAAAAA
Found at i:56071 original size:21 final size:21
Alignment explanation
Indices: 56030--56072 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
56020 TTAAAGATAA
*
56030 ATTATAAGTTTAATTATTTTT
1 ATTATAAGTTTAATTAATTTT
*
56051 ATTATAA-TTTTATCTAATTTT
1 ATTATAAGTTTAAT-TAATTTT
56072 A
1 A
56073 ATCATCATGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (21 bp):
ATTATAAGTTTAATTAATTTT
Found at i:58399 original size:14 final size:14
Alignment explanation
Indices: 58354--58391 Score: 76
Period size: 14 Copynumber: 2.7 Consensus size: 14
58344 TTTTTATTTA
58354 TTTAATTTCAGTCC
1 TTTAATTTCAGTCC
58368 TTTAATTTCAGTCC
1 TTTAATTTCAGTCC
58382 TTTAATTTCA
1 TTTAATTTCA
58392 TTACTTTAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.24, C:0.18, G:0.05, T:0.53
Consensus pattern (14 bp):
TTTAATTTCAGTCC
Found at i:58404 original size:14 final size:14
Alignment explanation
Indices: 58354--58404 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
58344 TTTTTATTTA
*
58354 TTTAATTTCAGTCC
1 TTTAATTTCAGTAC
*
58368 TTTAATTTCAGTCC
1 TTTAATTTCAGTAC
*
58382 TTTAATTTCATTAC
1 TTTAATTTCAGTAC
*
58396 TTTAGTTTC
1 TTTAATTTC
58405 CTATTTTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 34 1.00
ACGTcount: A:0.22, C:0.18, G:0.06, T:0.55
Consensus pattern (14 bp):
TTTAATTTCAGTAC
Found at i:60189 original size:12 final size:12
Alignment explanation
Indices: 60169--60228 Score: 59
Period size: 12 Copynumber: 4.8 Consensus size: 12
60159 AAAAAGAAAG
*
60169 AAAATAAAAATA
1 AAAAGAAAAATA
*
60181 AAAAGAAAAATG
1 AAAAGAAAAATA
60193 AAAAGAAAAATGAA
1 AAAAGAAAAAT--A
*
60207 AAAAGAAGCAA-A
1 AAAAGAA-AAATA
60219 AAAAGAAAAA
1 AAAAGAAAAA
60229 AATTAAAATA
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
11 2 0.05
12 29 0.73
14 7 0.17
15 2 0.05
ACGTcount: A:0.80, C:0.02, G:0.12, T:0.07
Consensus pattern (12 bp):
AAAAGAAAAATA
Found at i:60229 original size:19 final size:18
Alignment explanation
Indices: 60155--60229 Score: 66
Period size: 19 Copynumber: 4.1 Consensus size: 18
60145 AAAAAATAAT
60155 AAGAAAA-AAGAAAGAAAA
1 AAGAAAAGAA-AAAGAAAA
* *
60173 TA-AAAATAAAAAGAAAA
1 AAGAAAAGAAAAAGAAAA
*
60190 ATGAAAAGAAAAATGAAAA
1 AAGAAAAGAAAAA-GAAAA
60209 AAGAAGCAA-AAAAAGAAAA
1 AAGAA--AAGAAAAAGAAAA
60228 AA
1 AA
60230 ATTAAAATAA
Statistics
Matches: 47, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
17 12 0.26
18 12 0.26
19 16 0.34
20 5 0.11
21 2 0.04
ACGTcount: A:0.80, C:0.01, G:0.13, T:0.05
Consensus pattern (18 bp):
AAGAAAAGAAAAAGAAAA
Found at i:62382 original size:101 final size:101
Alignment explanation
Indices: 62186--62394 Score: 275
Period size: 101 Copynumber: 2.1 Consensus size: 101
62176 ACATGAACAT
* *
62186 TTGAGATTGTTTTTCTCAAAATCAATTTCATCTCACTTGAGACATTTTCCTTTGAAGCAAAAGTT
1 TTGAGATTGTTTTTCTCAAAATCAATTTCATCTCACTTGAGACATTTTCCTTGGAAGCAAAAGAT
* *
62251 TTGGAATTGCTTCTCATGAAACAAGATTTATCTCAC
66 TTGAAATTGCTTCACATGAAACAAGATTTATCTCAC
* *
62287 TTGAGATTGTTTTTCTTAAAATCAATTTCATCTCGCTTGAGACAATTTTCCCTTGGAA-CACAAA
1 TTGAGATTGTTTTTCTCAAAATCAATTTCATCTCACTTGAGAC-ATTTT-CCTTGGAAGCA-AAA
*
62351 -ATTTGAAATTG-TTCAC-TCGAACCAA-ATTTTATCTCAC
63 GATTTGAAATTGCTTCACAT-GAAACAAGA-TTTATCTCAC
62388 TTGAGAT
1 TTGAGAT
62395 AGCTTCTTTT
Statistics
Matches: 96, Mismatches: 7, Indels: 10
0.85 0.06 0.09
Matches are distributed among these distances:
100 2 0.02
101 68 0.71
102 16 0.17
103 10 0.10
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.39
Consensus pattern (101 bp):
TTGAGATTGTTTTTCTCAAAATCAATTTCATCTCACTTGAGACATTTTCCTTGGAAGCAAAAGAT
TTGAAATTGCTTCACATGAAACAAGATTTATCTCAC
Found at i:62822 original size:44 final size:45
Alignment explanation
Indices: 62745--62858 Score: 106
Period size: 44 Copynumber: 2.6 Consensus size: 45
62735 GTTCAATATT
* * * * * *
62745 TTGCTCCATTCTATCACAGAAGGAGGTAGATCAACA-TCAACATT-
1 TTGCTCGATTCCATCATAGAATGAGCTGGATCAACATTC-ACATTC
* * * *
62789 TTGTTCGATTCCATTATAGAATGAGCTGGATCAATATTCTCATTC
1 TTGCTCGATTCCATCATAGAATGAGCTGGATCAACATTCACATTC
*
62834 TTGCTCGATTCTATCATAGAATGAG
1 TTGCTCGATTCCATCATAGAATGAG
62859 GTAGATCGTC
Statistics
Matches: 55, Mismatches: 13, Indels: 3
0.77 0.18 0.04
Matches are distributed among these distances:
44 31 0.56
45 24 0.44
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (45 bp):
TTGCTCGATTCCATCATAGAATGAGCTGGATCAACATTCACATTC
Found at i:68158 original size:20 final size:19
Alignment explanation
Indices: 68120--68164 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
68110 GTTAAGAAAA
68120 ATATATAAAACAAACGTAT
1 ATATATAAAACAAACGTAT
* *
68139 ATATATATAACCAAATGTAT
1 ATATATA-AAACAAACGTAT
68159 ATATAT
1 ATATAT
68165 GTATGTATGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.53, C:0.09, G:0.04, T:0.33
Consensus pattern (19 bp):
ATATATAAAACAAACGTAT
Found at i:68415 original size:29 final size:30
Alignment explanation
Indices: 68391--68450 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
68381 GTGACCACTG
68391 AACT-TTCAATTGAATCAATCAGACCACCA
1 AACTATTCAATTGAATCAATCAGACCACCA
* * *
68420 AACTATTTAATTGATTCAATCAAACCACCA
1 AACTATTCAATTGAATCAATCAGACCACCA
68450 A
1 A
68451 CCGTTAGTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 4 0.15
30 23 0.85
ACGTcount: A:0.43, C:0.25, G:0.05, T:0.27
Consensus pattern (30 bp):
AACTATTCAATTGAATCAATCAGACCACCA
Found at i:69041 original size:29 final size:29
Alignment explanation
Indices: 68999--69062 Score: 110
Period size: 29 Copynumber: 2.2 Consensus size: 29
68989 GTCGAACCAA
*
68999 AATTTATTTGAAAATTATTAACCAAACCG
1 AATTAATTTGAAAATTATTAACCAAACCG
*
69028 AATTAATTTGAAAATTATTAACCGAACCG
1 AATTAATTTGAAAATTATTAACCAAACCG
69057 AATTAA
1 AATTAA
69063 CCAAATTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.47, C:0.12, G:0.08, T:0.33
Consensus pattern (29 bp):
AATTAATTTGAAAATTATTAACCAAACCG
Found at i:69178 original size:29 final size:30
Alignment explanation
Indices: 69135--69191 Score: 98
Period size: 29 Copynumber: 1.9 Consensus size: 30
69125 CGTTTAATCG
*
69135 AACCAAAATTTATTTGAAAATTATTAACAT
1 AACCAAAATTAATTTGAAAATTATTAACAT
69165 AACC-AAATTAATTTGAAAATTATTAAC
1 AACCAAAATTAATTTGAAAATTATTAAC
69192 CAAACTGAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 22 0.85
30 4 0.15
ACGTcount: A:0.51, C:0.11, G:0.04, T:0.35
Consensus pattern (30 bp):
AACCAAAATTAATTTGAAAATTATTAACAT
Found at i:69236 original size:14 final size:14
Alignment explanation
Indices: 69217--69243 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
69207 GAAGAAAAAA
69217 TTCGGTTAATTTGG
1 TTCGGTTAATTTGG
69231 TTCGGTTAATTTG
1 TTCGGTTAATTTG
69244 AAAATTATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.07, G:0.26, T:0.52
Consensus pattern (14 bp):
TTCGGTTAATTTGG
Found at i:69780 original size:245 final size:245
Alignment explanation
Indices: 69319--69785 Score: 767
Period size: 246 Copynumber: 1.9 Consensus size: 245
69309 TTTGATTCGG
* *
69319 TTAATCGAACCAAAATTATTTGAAAATTATTAACTGAACCGAACAAATTTCAGTTAATTCTGTCA
1 TTAATCGAACCAAAATTATTTGAAAATTATTAACTCAACCAAACAAATTTCAGTTAATTCTGTCA
* * *
69384 ATTTTCGAATTAACGATTTTTTTTAAATTTTCTACTATATAAAAATTGAATATTTTTAATTCAAA
66 ATTTTCGAATTAACAAATTTTTTAAAATTTTCTACTATATAAAAATTGAATATTTTTAATTC-AA
* * * *
69449 AAAACGTTTACAATTAATTTAAATAATTATTTGTTTAAACAACTAATTTGTTTAATTTTTTATCC
130 AAAACATTTACAATTAATTTAAATAATAATTTGTTTAAACAAATAATTTGTTTAATTATTTATCC
69514 TTAACAAACCTTTAAAAGACAAATACATCAAACCGATTTTTTCTTTAACCA
195 TTAACAAACCTTTAAAAGACAAATACATCAAACCGATTTTTTCTTTAACCA
** * *
69565 TTAATCGAACCGAATTTTATTTGAAAATTATTAA-TCAACCAAACAAATTTCGGTTAGTTCTGTC
1 TTAATCGAACC-AAAATTATTTGAAAATTATTAACTCAACCAAACAAATTTCAGTTAATTCTGTC
69629 AATTTTCGAATTAACAAATTTTTTAAAATTTTCTACTATATAAAAATTGAATATTTTTAATTC-A
65 AATTTTCGAATTAACAAATTTTTTAAAATTTTCTACTATATAAAAATTGAATATTTTTAATTCAA
69693 AAAACTATTTACAATTAATTTAAATAATAATTTGTTTAAACAAATAATTTGTTTAATTATTTATC
130 AAAAC-ATTTACAATTAATTTAAATAATAATTTGTTTAAACAAATAATTTGTTTAATTATTTATC
*
69758 CTTAAGAAACCTTTAAAAGACAAATACA
194 CTTAACAAACCTTTAAAAGACAAATACA
69786 AATTGTTGTA
Statistics
Matches: 205, Mismatches: 14, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
244 6 0.03
245 82 0.40
246 97 0.47
247 20 0.10
ACGTcount: A:0.41, C:0.12, G:0.06, T:0.41
Consensus pattern (245 bp):
TTAATCGAACCAAAATTATTTGAAAATTATTAACTCAACCAAACAAATTTCAGTTAATTCTGTCA
ATTTTCGAATTAACAAATTTTTTAAAATTTTCTACTATATAAAAATTGAATATTTTTAATTCAAA
AAACATTTACAATTAATTTAAATAATAATTTGTTTAAACAAATAATTTGTTTAATTATTTATCCT
TAACAAACCTTTAAAAGACAAATACATCAAACCGATTTTTTCTTTAACCA
Found at i:71062 original size:17 final size:18
Alignment explanation
Indices: 71026--71117 Score: 57
Period size: 18 Copynumber: 5.0 Consensus size: 18
71016 TGTTAGAGGG
*
71026 AAAAAATGAATAAATGAA
1 AAAAAATGAATAAATAAA
*
71044 AAAAAATGAA-GAATAAA
1 AAAAAATGAATAAATAAA
*
71061 AATAAGTAA-AAATAAATAAA
1 AA-AA--AATGAATAAATAAA
*
71081 AATAAAA-GGA-AAATAAA
1 AA-AAAATGAATAAATAAA
*
71098 TAAATAAATAAATAAATAAA
1 -AAA-AAATGAATAAATAAA
71118 TGAAATATTA
Statistics
Matches: 58, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
17 15 0.26
18 20 0.34
19 3 0.05
20 20 0.34
ACGTcount: A:0.75, C:0.00, G:0.08, T:0.17
Consensus pattern (18 bp):
AAAAAATGAATAAATAAA
Found at i:71070 original size:10 final size:10
Alignment explanation
Indices: 71055--71113 Score: 66
Period size: 10 Copynumber: 5.6 Consensus size: 10
71045 AAAAATGAAG
71055 AATAAAAATA
1 AATAAAAATA
*
71065 AGTAAAAATA
1 AATAAAAATA
71075 AATAAAAATA
1 AATAAAAATA
71085 AA-AGGAAAATA
1 AATA--AAAATA
71096 AATAAATAAATA
1 AAT-AA-AAATA
71108 AATAAA
1 AATAAA
71114 TAAATGAAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
9 1 0.02
10 21 0.50
11 11 0.26
12 8 0.19
13 1 0.02
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.19
Consensus pattern (10 bp):
AATAAAAATA
Found at i:71086 original size:16 final size:16
Alignment explanation
Indices: 71037--71117 Score: 53
Period size: 16 Copynumber: 5.1 Consensus size: 16
71027 AAAAATGAAT
71037 AAATGAAAAA-AAATGAA
1 AAAT-AAAAATAAAT-AA
* *
71054 GAATAAAAATAAGTAA
1 AAATAAAAATAAATAA
71070 AAATAAATAA-AAAT-A
1 AAATAAA-AATAAATAA
**
71085 AAAGGAAAATAAATAA
1 AAATAAAAATAAATAA
*
71101 ATAA-ATAAATAAATAA
1 A-AATAAAAATAAATAA
71117 A
1 A
71118 TGAAATATTA
Statistics
Matches: 51, Mismatches: 8, Indels: 11
0.73 0.11 0.16
Matches are distributed among these distances:
14 2 0.04
15 10 0.20
16 29 0.57
17 10 0.20
ACGTcount: A:0.75, C:0.00, G:0.07, T:0.17
Consensus pattern (16 bp):
AAATAAAAATAAATAA
Found at i:71098 original size:4 final size:4
Alignment explanation
Indices: 71091--71124 Score: 59
Period size: 4 Copynumber: 8.2 Consensus size: 4
71081 AATAAAAGGA
71091 AAAT AAAT AAAT AAAT AAAT AAAT AAAT GAAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT -AAAT A
71125 TTATATATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 25 0.86
5 4 0.14
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:71432 original size:2 final size:2
Alignment explanation
Indices: 71427--71525 Score: 102
Period size: 2 Copynumber: 52.5 Consensus size: 2
71417 ATTTTAAAAA
71427 AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * *
71468 AT AG AT AT AT AT AT AT AA AA AT A- AT AT CT A- AA AA AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
71508 AT AT A- AT A- AT A- AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
71526 GTGTAAAAAA
Statistics
Matches: 84, Mismatches: 7, Indels: 12
0.82 0.07 0.12
Matches are distributed among these distances:
1 6 0.07
2 78 0.93
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (2 bp):
AT
Found at i:71509 original size:15 final size:15
Alignment explanation
Indices: 71421--71535 Score: 83
Period size: 16 Copynumber: 7.5 Consensus size: 15
71411 TAAAATATTT
71421 TAAAAAATATATATA
1 TAAAAAATATATATA
* *
71436 T-ATATATATATAT-
1 TAAAAAATATATATA
* *
71449 TATATATATATATATA
1 TA-AAAAATATATATA
* *
71465 TATATAGATATATATA
1 TA-AAAAATATATATA
*
71481 TATAAAAATA-ATATC
1 TA-AAAAATATATATA
71496 TAAAAAATATATATA
1 TAAAAAATATATATA
*
71511 TAATAATAATATATAGTG
1 TAA-AA-AATATATA-TA
71529 TAAAAAA
1 TAAAAAA
71536 ATCAATTGAA
Statistics
Matches: 85, Mismatches: 8, Indels: 13
0.80 0.08 0.12
Matches are distributed among these distances:
13 1 0.01
14 17 0.20
15 26 0.31
16 27 0.32
17 10 0.12
18 4 0.05
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.39
Consensus pattern (15 bp):
TAAAAAATATATATA
Found at i:72071 original size:37 final size:37
Alignment explanation
Indices: 71998--72090 Score: 123
Period size: 37 Copynumber: 2.5 Consensus size: 37
71988 GGATCCTATC
* * * * *
71998 TTAGGAGTTTAAATCATAGTAGAACTCTATCCTATTT
1 TTAGGAGTTTGAATCCTAGCAAAACTCTATCATATTT
* *
72035 TTAGGAGTTTGAATCCTAGCAAAATTTTATCATATTT
1 TTAGGAGTTTGAATCCTAGCAAAACTCTATCATATTT
72072 TTAGGAGTTTGAATCCTAG
1 TTAGGAGTTTGAATCCTAG
72091 TAGGACAAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 49 1.00
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.41
Consensus pattern (37 bp):
TTAGGAGTTTGAATCCTAGCAAAACTCTATCATATTT
Found at i:72968 original size:105 final size:106
Alignment explanation
Indices: 72824--73872 Score: 1312
Period size: 105 Copynumber: 10.0 Consensus size: 106
72814 GCATTGTTCT
* * **
72824 GAGTCCAATATCCTCCG-TCGTGAAGTTAAAATTGGCTCTGGAACCT-GAAAATTGTTTGTTGAC
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCT-GAAATTGGAAAATTGTTTGTTGAC
* * * ** * *
72887 AACCAACCGTCCCTTCGTTGTGAAGTTGAACTTGTTTTGTATC
64 AACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
72930 GA-TCCAATAACATTCGCTGTGAAGTTGAAATTGACTCTG-AA-T-G-AAA-T-TTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGAAAATTGTTTGTTGACAA
* * * * * * *
72988 TCAGCCGCCCCTTCGTCATGAAGATT-AGCTTGTGTTGCCTTG
66 CCAGCGGTCCCTTCGTCGTGAAG-TTGAACTTGCGTTGTC-TG
* * * * * *
73030 G-GTTCAAGATCCTTCGCTGAGAAGTTAAAATTGGCTCTGAAATTGGAAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGAAAATTGTTTGTTGACAA
*
73094 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
73135 GAGTCCAATATCCTACGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTATTGA-AA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGAAAATTGTTTGTTGACAA
73199 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
** * *
73240 GAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTAAAATT-GAGAAGTTGTTTGTTGACA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGA-AAATTGTTTGTTGACA
*
73304 ACCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
73346 AAGTCCAAAATCCTTCACTGTGAAGTTGAAATTGGCTCTGAAATT-GAGAAGTTGTTTGTTGACA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGA-AAATTGTTTGTTGACA
* * * *
73410 ACCAACGGTCCCTTTGTTGTGAAGTTGAACTTGCGTTGTTTG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
73452 GAGT-CAATATCCTTCGCTGTGAAGTTAAAATTGGCTCTGAAATTGGGAAGTTGTTT-TTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGAAAATTGTTTGTTGACAA
*
73515 CCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCG-TGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
73555 GAGTCCAATATCTTTCGTTGTGAAG-TGAAATTGGCTCTGAAATTGGAAAGTTGTTT-ATGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGAAAATTGTTTGTTGACAA
*
73618 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
73659 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGATCTGAAATTGGAAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGAAAATTGTTTGTTGACAA
* *
73724 CCAACGGTCCCTTCGTCGTGAAGTTGAAC-TGCATTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
73764 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGAAAATTG-TTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGAAAATTGTTTGTTGACAA
* * * ** *
73828 CCAGCCGTCCCTTCGTTGTGAAGTTGTACTTATGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
73869 GAGT
1 GAGT
73873 GGCACGATAT
Statistics
Matches: 829, Mismatches: 94, Indels: 41
0.86 0.10 0.04
Matches are distributed among these distances:
99 38 0.05
100 35 0.04
101 5 0.01
102 3 0.00
103 78 0.09
104 124 0.15
105 275 0.33
106 271 0.33
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGAAAATTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:73701 original size:313 final size:314
Alignment explanation
Indices: 72824--73858 Score: 1357
Period size: 313 Copynumber: 3.3 Consensus size: 314
72814 GCATTGTTCT
* ** *
72824 GAGTCCAATATCCTCCG-TCGTGAAGTTAAAATTGGCTCTGGAACCT-GAAAATTGTTTGTTGAC
1 GAGTCCAATATCCTTCGCT-GTGAAGTTAAAATTGGCTCT-GAAATTGGAAAATTGTTTATTGAC
* ** * * * *
72887 AACCAACCGTCCCTTCGTTGTGAAGTTGAACTTGTTTTGTATCGA-TCCAATAACATTCGCTGTG
64 AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTG-CGTGTCTGGAGTCCAATATCATTCGTTGTG
* * * * *
72951 AAGTTGAAATTGACTCTG-AA-TGAAA-TT-TTGTTGACAATCAGCCGCCCCTTCGTCATGAAGA
128 AAGTTGAAATTGGCTCTGAAATTGAAAGTTGTT-TTGACAACCAGCGGTCCCTTCGTCGTGAAG-
* * * * * *
73012 TT-AGCTTGTGTTGCCTTGG-GTTCAAGATCCTTCGCTGAGAAGTTAAAATTGGCTCTGAAATTG
191 TTGAACTTGTGTTGTC-TGGAGTCCAAAATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTG
*
73075 GAAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT-
255 GAAAGTTGTTTATTGACAACCAACGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT-TTG
* * * *
73135 GAGTCCAATATCCTACGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTATTGA-AA
1 GAGTCCAATATCCTTCGCTGTGAAGTTAAAATTGGCTCTGAAATTGGAAAATTGTTTATTGACAA
* * * *
73199 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCATTGTGAA
66 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGCG-TGTCTGGAGTCCAATATCATTCGTTGTGAA
* *
73264 GTTGAAATTGGCTCTAAAATTGAGAAGTTGTTTGTTGACAACCAGTGGTCCCTTCGTCGTGAAGT
130 GTTGAAATTGGCTCTGAAATTGA-AAGTTG-TT-TTGACAACCAGCGGTCCCTTCGTCGTGAAGT
* * *
73329 TGAACTTGCGTTGTCTGAAGTCCAAAATCCTTCACTGTGAAGTTGAAATTGGCTCTGAAATT-GA
192 TGAACTTGTGTTGTCTGGAGTCCAAAATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGA
* * *
73393 GAAGTTGTTTGTTGACAACCAACGGTCCCTTTGTTGTGAAGTTGAACTTGCGTTGTTTG
257 -AAGTTGTTTATTGACAACCAACGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTTTG
* *
73452 GAGT-CAATATCCTTCGCTGTGAAGTTAAAATTGGCTCTGAAATTGGGAAGTTGTTT-TTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTAAAATTGGCTCTGAAATTGGAAAATTGTTTATTGACAA
* *
73515 CCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTGTCTGGAGTCCAATATCTTTCGTTGTGAAG
66 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGCGTGTCTGGAGTCCAATATCATTCGTTGTGAAG
73580 -TGAAATTGGCTCTGAAATTGGAAAGTTGTTTATGACAACCAGCGGTCCCTTCGTCGTGAAGTTG
131 TTGAAATTGGCTCTGAAATT-GAAAGTTGTTT-TGACAACCAGCGGTCCCTTCGTCGTGAAGTTG
* *
73644 AACTTGTGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGATCTGAAATTGGAAA
194 AACTTGTGTTGTCTGGAGTCCAAAATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGAAA
* * *
73709 ATTGTTTATTGACAACCAACGGTCCCTTCGTCGTGAAGTTGAAC-TGCATTGTCTG
259 GTTGTTTATTGACAACCAACGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTTTG
* * *
73764 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGAAAATTG-TTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTAAAATTGGCTCTGAAATTGGAAAATTGTTTATTGACAA
*
73828 CCAGCCGTCCCTTCGTTGTGAAGTTGTACTT
66 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTT
73859 ATGTTGTCTT
Statistics
Matches: 640, Mismatches: 64, Indels: 38
0.86 0.09 0.05
Matches are distributed among these distances:
310 41 0.06
311 79 0.12
312 19 0.03
313 214 0.33
314 28 0.04
315 37 0.06
316 91 0.14
317 131 0.20
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (314 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTAAAATTGGCTCTGAAATTGGAAAATTGTTTATTGACAA
CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGCGTGTCTGGAGTCCAATATCATTCGTTGTGAAG
TTGAAATTGGCTCTGAAATTGAAAGTTGTTTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAA
CTTGTGTTGTCTGGAGTCCAAAATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGAAAGT
TGTTTATTGACAACCAACGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTTTG
Found at i:74738 original size:21 final size:22
Alignment explanation
Indices: 74682--74756 Score: 118
Period size: 22 Copynumber: 3.5 Consensus size: 22
74672 TTATGTTTGG
74682 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
74704 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
74726 TCATAGG-TTGGCA-TTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
74746 TCAACGGTTTG
1 TCAAAGGTTTG
74757 ATGGGGTAGC
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.24
21 9 0.18
22 28 0.57
ACGTcount: A:0.21, C:0.15, G:0.28, T:0.36
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:75358 original size:17 final size:18
Alignment explanation
Indices: 75338--75396 Score: 59
Period size: 17 Copynumber: 3.2 Consensus size: 18
75328 TCTTTTTGAT
75338 TTTTGTTCTTTTT-TTTC
1 TTTTGTTCTTTTTCTTTC
75355 TTTTGTTTCTCTTTTTCTTTC
1 TTTTG--T-TCTTTTTCTTTC
* *
75376 TTTTCTTCTTTTGC-TTC
1 TTTTGTTCTTTTTCTTTC
75393 TTTT
1 TTTT
75397 TTTTTTCTTG
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
17 12 0.33
18 7 0.19
19 2 0.06
20 7 0.19
21 8 0.22
ACGTcount: A:0.00, C:0.17, G:0.05, T:0.78
Consensus pattern (18 bp):
TTTTGTTCTTTTTCTTTC
Found at i:75367 original size:11 final size:9
Alignment explanation
Indices: 75337--75400 Score: 58
Period size: 9 Copynumber: 6.9 Consensus size: 9
75327 TTCTTTTTGA
*
75337 TTTTTGTTC
1 TTTTTTTTC
75346 TTTTTTTTC
1 TTTTTTTTC
75355 TTTTGTTTCTC
1 TTTT-TTT-TC
75366 TTTTTCTTTC
1 TTTTT-TTTC
*
75376 -TTTTCTTC
1 TTTTTTTTC
**
75384 TTTTGCTTC
1 TTTTTTTTC
75393 TTTTTTTT
1 TTTTTTTT
75401 TTCTTGATTG
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
8 3 0.07
9 29 0.63
10 6 0.13
11 8 0.17
ACGTcount: A:0.00, C:0.16, G:0.05, T:0.80
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:75379 original size:29 final size:28
Alignment explanation
Indices: 75347--75405 Score: 82
Period size: 29 Copynumber: 2.1 Consensus size: 28
75337 TTTTTGTTCT
* *
75347 TTTTTTTCTTTTGTTTCTCTTTTTCTTTC
1 TTTTCTTCTTTTGCTTCT-TTTTTCTTTC
*
75376 TTTTCTTCTTTTGCTTCTTTTTTTTTTC
1 TTTTCTTCTTTTGCTTCTTTTTTCTTTC
75404 TT
1 TT
75406 GATTGGATCT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 11 0.41
29 16 0.59
ACGTcount: A:0.00, C:0.17, G:0.03, T:0.80
Consensus pattern (28 bp):
TTTTCTTCTTTTGCTTCTTTTTTCTTTC
Found at i:75384 original size:20 final size:20
Alignment explanation
Indices: 75344--75384 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
75334 TGATTTTTGT
*
75344 TCTTTTTTTTCTTTTGTTTC
1 TCTTTTTTTTCTTTTGCTTC
75364 TCTTTTTCTTTCTTTT-CTTC
1 TCTTTTT-TTTCTTTTGCTTC
75384 T
1 T
75385 TTTGCTTCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (20 bp):
TCTTTTTTTTCTTTTGCTTC
Done.