Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008260.1 Hibiscus syriacus cultivar Beakdansim tig00110913_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: 75047
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Found at i:1987 original size:20 final size:21
Alignment explanation
Indices: 1958--1999 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
1948 GAAAGATTAA
*
1958 TTTTATTCATGATTGTTGTTT
1 TTTTATTCATGATTATTGTTT
1979 TTTTA-TCATGATTATTGTTT
1 TTTTATTCATGATTATTGTTT
1999 T
1 T
2000 CTCGTTGCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.17, C:0.05, G:0.12, T:0.67
Consensus pattern (21 bp):
TTTTATTCATGATTATTGTTT
Found at i:2458 original size:2 final size:2
Alignment explanation
Indices: 2451--2529 Score: 149
Period size: 2 Copynumber: 39.5 Consensus size: 2
2441 AACTGATTAG
*
2451 TA TA TA TA TA TA TA TA TA TA TA TA TA TA GA 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
2493 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2530 GATTCTCCTG
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 75 1.00
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (2 bp):
TA
Found at i:5403 original size:15 final size:16
Alignment explanation
Indices: 5374--5412 Score: 71
Period size: 15 Copynumber: 2.5 Consensus size: 16
5364 ATAACGACGA
5374 AACCAGAGAAATCCAC
1 AACCAGAGAAATCCAC
5390 AACCAGAG-AATCCAC
1 AACCAGAGAAATCCAC
5405 AACCAGAG
1 AACCAGAG
5413 TCTAAAATCC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 15 0.65
16 8 0.35
ACGTcount: A:0.49, C:0.31, G:0.15, T:0.05
Consensus pattern (16 bp):
AACCAGAGAAATCCAC
Found at i:18385 original size:11 final size:11
Alignment explanation
Indices: 18365--18433 Score: 50
Period size: 11 Copynumber: 5.8 Consensus size: 11
18355 ATTTTGCTTG
18365 AAGAAAAAAAA
1 AAGAAAAAAAA
18376 AAGAAGAAAAATGA
1 AAGAA-AAAAA--A
**
18390 GTGAAAATGAAAA
1 AAGAAAA--AAAA
*
18403 AATAAAAAAAA
1 AAGAAAAAAAA
18414 AA-AAAAAAAA
1 AAGAAAAAAAA
18424 AATGAAAAAA
1 AA-GAAAAAA
18434 TGGAAAAAAG
Statistics
Matches: 46, Mismatches: 5, Indels: 13
0.72 0.08 0.20
Matches are distributed among these distances:
10 10 0.22
11 11 0.24
12 11 0.24
13 7 0.15
14 4 0.09
15 3 0.07
ACGTcount: A:0.81, C:0.00, G:0.12, T:0.07
Consensus pattern (11 bp):
AAGAAAAAAAA
Found at i:18404 original size:8 final size:8
Alignment explanation
Indices: 18393--18442 Score: 52
Period size: 8 Copynumber: 6.5 Consensus size: 8
18383 AAAATGAGTG
18393 AAAATGAA
1 AAAATGAA
18401 AAAAT-AA
1 AAAATGAA
18408 AAAA--AA
1 AAAATGAA
**
18414 AAAAAAAA
1 AAAATGAA
18422 AAAATGAA
1 AAAATGAA
18430 AAAATGGAA
1 AAAAT-GAA
18439 AAAA
1 AAAA
18443 GAAGGGTTCA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
6 6 0.16
7 6 0.16
8 18 0.49
9 7 0.19
ACGTcount: A:0.84, C:0.00, G:0.08, T:0.08
Consensus pattern (8 bp):
AAAATGAA
Found at i:19415 original size:55 final size:55
Alignment explanation
Indices: 19346--20103 Score: 863
Period size: 55 Copynumber: 13.9 Consensus size: 55
19336 AGGTTTCCCA
*
19346 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
* * *
19401 ACGATGGTTGAAGATTGTTCGAGTCTCATACTCTCTTAAGAAATAGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
* * *
19456 ACGATTGATGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATGGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
*
19511 ACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGCAGAAATAGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
* * *
19566 ACGATTGATGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATGGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
* * * *
19621 ACGATTGATGAAAATTGTTCGAGTCTTATACTCTCTGCATAAATAGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
* * *
19676 ACGACTGTTGAAGATTGTTGGAGTCTTATACTCTCTGCAGAAATAGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
* * *
19731 ACGATTGATGAAGATTGTTCAAGTCTTATACTCTCTGAAGGAATAGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
* * * * * *
19786 ACGATTGATGAAGATTCTTCAAGT-TCCATACTCCCT-AGAGAAAGAGGGAGC-GA-
1 ACGATTGTTGAAGATTGTTCGAGTCT-TATACTCTCTGA-AGAAATAGGGAGCAGAC
* * * * *
19839 ACCCA--GTTGAAGA-TGTTCGAGT-TCCATACTC-CTTAAAGAAAGA-AGAGC-GAAC
1 A-CGATTGTTGAAGATTGTTCGAGTCT-TATACTCTC-TGAAGAAATAGGGAGCAG-AC
* * * * *
19891 CCG--T-TTGAAGAGATGTTCGAGT-TCCATACTCCCT-AGAGAAATAGGGAAC-GA-
1 ACGATTGTTGAAGA-TTGTTCGAGTCT-TATACTCTCTGA-AGAAATAGGGAGCAGAC
* *
19942 ACCCATTTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGAC
1 A-CGA-TTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
* * * *
19999 GCGATCGTTGAAGATTGTTCGAGTCCTATACTCTCTGAAGAAATAGGGGGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
* *
20054 AAGTTTGTTGAAGA-TGATTC-AGTCTTATACTCTCTGAAGAAATAGGGAGC
1 ACGATTGTTGAAGATTG-TTCGAGTCTTATACTCTCTGAAGAAATAGGGAGC
20104 GAACCCATTT
Statistics
Matches: 616, Mismatches: 64, Indels: 47
0.85 0.09 0.06
Matches are distributed among these distances:
50 13 0.02
51 27 0.04
52 35 0.06
53 6 0.01
54 36 0.06
55 486 0.79
56 13 0.02
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.27
Consensus pattern (55 bp):
ACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
Found at i:19870 original size:51 final size:51
Alignment explanation
Indices: 19807--19967 Score: 200
Period size: 52 Copynumber: 3.1 Consensus size: 51
19797 AGATTCTTCA
19807 AGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCAGTTGAAGATGTTCG
1 AGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCAGTTGAAGATGTTCG
* * *
19858 AGTTCCATACTCCTTAAAGAAAGA-AGAGCGAACCC-GTTTGAAGAGATGTTCG
1 AGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCAG-TTG-A-AGATGTTCG
* *
19910 AGTTCCATACTCCCTAGAGAAATAGGGAACGAACCCATTTGTTGAAGATTGTTCG
1 AGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCA---GTTGAAGA-TGTTCG
19965 AGT
1 AGT
19968 CTTATACTCT
Statistics
Matches: 93, Mismatches: 8, Indels: 14
0.81 0.07 0.12
Matches are distributed among these distances:
49 1 0.01
50 13 0.14
51 23 0.25
52 30 0.32
53 9 0.10
54 3 0.03
55 10 0.11
56 3 0.03
57 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.24
Consensus pattern (51 bp):
AGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCAGTTGAAGATGTTCG
Found at i:21229 original size:20 final size:16
Alignment explanation
Indices: 21180--21219 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
21170 ATAACGACGA
21180 AACCAGAGAAATCCAC
1 AACCAGAGAAATCCAC
21196 AACCAGAGAAATCCAC
1 AACCAGAGAAATCCAC
21212 AACCAGAG
1 AACCAGAG
21220 TCTAAAATCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.50, C:0.30, G:0.15, T:0.05
Consensus pattern (16 bp):
AACCAGAGAAATCCAC
Found at i:27716 original size:69 final size:69
Alignment explanation
Indices: 27600--27735 Score: 200
Period size: 69 Copynumber: 2.0 Consensus size: 69
27590 GCCTGGATTG
* * * *
27600 AGGATTATCCGGCATCGTTATTGCTTCGTCGAGGTCGAATTGATGAGTGATATAGGGGATGATTA
1 AGGATTATCCGGCATCGTAATTGCATCGTCGAGGTCGAATTGATGAGTGAGATAAGGGATGATTA
27665 CAGA
66 CAGA
* * * *
27669 AGGATTTTCCGGCATCGTAATTGCATCGTCGAGGTCGAATTGCTGAGTGGGATAAGGGATTATTA
1 AGGATTATCCGGCATCGTAATTGCATCGTCGAGGTCGAATTGATGAGTGAGATAAGGGATGATTA
27734 CA
66 CA
27736 AAGTTATTGT
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
69 59 1.00
ACGTcount: A:0.26, C:0.14, G:0.30, T:0.30
Consensus pattern (69 bp):
AGGATTATCCGGCATCGTAATTGCATCGTCGAGGTCGAATTGATGAGTGAGATAAGGGATGATTA
CAGA
Found at i:27800 original size:2 final size:2
Alignment explanation
Indices: 27793--27823 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
27783 TCGCCGGAGT
*
27793 GA GA GA GA GA GA GA GA GA GA GA GG GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
27824 GAGTTTAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.55, T:0.00
Consensus pattern (2 bp):
GA
Found at i:28711 original size:23 final size:23
Alignment explanation
Indices: 28684--28727 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
28674 CAAATGACCG
28684 AAAACATACCATAAAGACAGAGA
1 AAAACATACCATAAAGACAGAGA
* *
28707 AAAACCTATCATAAAGACAGA
1 AAAACATACCATAAAGACAGA
28728 ATAATGCGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.59, C:0.18, G:0.11, T:0.11
Consensus pattern (23 bp):
AAAACATACCATAAAGACAGAGA
Found at i:28748 original size:22 final size:23
Alignment explanation
Indices: 28716--28770 Score: 76
Period size: 22 Copynumber: 2.4 Consensus size: 23
28706 AAAAACCTAT
*
28716 CATAAAGACAGAATAATGCGTGC
1 CATAAAGACAGAAGAATGCGTGC
* *
28739 TAT-AAGACAGAAGAATGTGTGC
1 CATAAAGACAGAAGAATGCGTGC
28761 CATAAAGACA
1 CATAAAGACA
28771 TAATTATTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 19 0.70
23 8 0.30
ACGTcount: A:0.45, C:0.15, G:0.22, T:0.18
Consensus pattern (23 bp):
CATAAAGACAGAAGAATGCGTGC
Found at i:29575 original size:17 final size:17
Alignment explanation
Indices: 29553--29585 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
29543 ATAGTATTCA
*
29553 CGATAAATGATCATTAC
1 CGATAAATAATCATTAC
29570 CGATAAATAATCATTA
1 CGATAAATAATCATTA
29586 TTAAAAATAT
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:0.45, C:0.15, G:0.09, T:0.30
Consensus pattern (17 bp):
CGATAAATAATCATTAC
Found at i:34211 original size:69 final size:69
Alignment explanation
Indices: 34086--34222 Score: 168
Period size: 69 Copynumber: 2.0 Consensus size: 69
34076 CCTGGCTTGA
* * * *
34086 GGGTTTTCCGACATCGTAATAGCTTCGTCGAGTTCGAATTGATGAGATAGGAAAGGGATCATCAA
1 GGGTTTTCCGACATCGTAATAGCGTCGTCGAGGTCGAATTGATAAGAGAGGAAAGGGATCATCAA
34151 AGAG
66 AGAG
* * * * * *
34155 GGGTTTTCCGGCATCGTGATTGCGTCGTCGAGGTCGAATTGATAAGCGA-GACAAGGGGTTATCA
1 GGGTTTTCCGACATCGTAATAGCGTCGTCGAGGTCGAATTGATAAGAGAGGA-AAGGGATCATCA
34219 AAGA
65 AAGA
34223 ATCATTGTTG
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
68 2 0.04
69 55 0.96
ACGTcount: A:0.28, C:0.15, G:0.31, T:0.26
Consensus pattern (69 bp):
GGGTTTTCCGACATCGTAATAGCGTCGTCGAGGTCGAATTGATAAGAGAGGAAAGGGATCATCAA
AGAG
Found at i:36307 original size:21 final size:21
Alignment explanation
Indices: 36283--36328 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
36273 ACTGACCACA
36283 ATGCTCGAGAAACAAACAAAC
1 ATGCTCGAGAAACAAACAAAC
36304 ATGCTCGAGAAACAAACAAAC
1 ATGCTCGAGAAACAAACAAAC
36325 ATGC
1 ATGC
36329 AACCAAGAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.50, C:0.24, G:0.15, T:0.11
Consensus pattern (21 bp):
ATGCTCGAGAAACAAACAAAC
Found at i:37402 original size:16 final size:16
Alignment explanation
Indices: 37381--37443 Score: 90
Period size: 16 Copynumber: 3.9 Consensus size: 16
37371 TTACCCGACC
37381 TGTTTTCAACCTGACT
1 TGTTTTCAACCTGACT
* *
37397 TGTTTTCAACTTGACA
1 TGTTTTCAACCTGACT
*
37413 TGTTTTTAACCTGACT
1 TGTTTTCAACCTGACT
*
37429 TGTTTTTAACCTGAC
1 TGTTTTCAACCTGAC
37444 CTGTAAATGA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 42 1.00
ACGTcount: A:0.21, C:0.21, G:0.13, T:0.46
Consensus pattern (16 bp):
TGTTTTCAACCTGACT
Found at i:37646 original size:13 final size:13
Alignment explanation
Indices: 37630--37656 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
37620 GAACTATTAT
37630 ATAAAATTATTTA
1 ATAAAATTATTTA
37643 ATAAAATTATTTA
1 ATAAAATTATTTA
37656 A
1 A
37657 ATGTAAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATAAAATTATTTA
Found at i:37804 original size:15 final size:15
Alignment explanation
Indices: 37784--37849 Score: 64
Period size: 15 Copynumber: 4.4 Consensus size: 15
37774 TGGCAATAAA
37784 ATAATAATTAAATTG
1 ATAATAATTAAATTG
* *
37799 ATAATAACTGAA-TG
1 ATAATAATTAAATTG
* *
37813 TTAAT-ATTAAACATG
1 ATAATAATTAAA-TTG
37828 ATTAATAATTAAATTG
1 A-TAATAATTAAATTG
37844 ATAATA
1 ATAATA
37850 GCTGAATATT
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
13 4 0.10
14 6 0.15
15 17 0.43
16 7 0.17
17 6 0.15
ACGTcount: A:0.52, C:0.03, G:0.08, T:0.38
Consensus pattern (15 bp):
ATAATAATTAAATTG
Found at i:38644 original size:20 final size:20
Alignment explanation
Indices: 38619--38663 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
38609 AACCCTTACA
**
38619 AATATCAAGTAGAAACAAAC
1 AATATCAAACAGAAACAAAC
38639 AATATCAAACAGAAACAAAC
1 AATATCAAACAGAAACAAAC
38659 AATAT
1 AATAT
38664 AAAATAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.62, C:0.16, G:0.07, T:0.16
Consensus pattern (20 bp):
AATATCAAACAGAAACAAAC
Found at i:38672 original size:20 final size:20
Alignment explanation
Indices: 38628--38672 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
38618 AAATATCAAG
*
38628 TAGAAACAAACAATATCAAA
1 TAGAAACAAACAATATAAAA
*
38648 CAGAAACAAACAATATAAAA
1 TAGAAACAAACAATATAAAA
38668 TAGAA
1 TAGAA
38673 TAATGCAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.67, C:0.13, G:0.07, T:0.13
Consensus pattern (20 bp):
TAGAAACAAACAATATAAAA
Found at i:40230 original size:23 final size:23
Alignment explanation
Indices: 40204--40268 Score: 64
Period size: 23 Copynumber: 2.9 Consensus size: 23
40194 AAAATAATTA
40204 TATATTTATAATTAATATTAACT
1 TATATTTATAATTAATATTAACT
* **
40227 TATATTAAT-A-TAATA-TAGTT
1 TATATTTATAATTAATATTAACT
*
40247 TATAATTTGTAATTAATATTAA
1 TAT-ATTTATAATTAATATTAA
40269 TATAAAATAT
Statistics
Matches: 32, Mismatches: 6, Indels: 7
0.71 0.13 0.16
Matches are distributed among these distances:
20 6 0.19
21 9 0.28
22 2 0.06
23 13 0.41
24 2 0.06
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.51
Consensus pattern (23 bp):
TATATTTATAATTAATATTAACT
Found at i:40295 original size:31 final size:30
Alignment explanation
Indices: 40257--40407 Score: 107
Period size: 31 Copynumber: 5.0 Consensus size: 30
40247 TATAATTTGT
*
40257 AATTAATATTAATATAAAATATAGTCTATAA
1 AATTAATATTAATATAAACTATAGT-TATAA
40288 AATTAATATTAATATAAACTATATGTTAT-A
1 AATTAATATTAATATAAACTATA-GTTATAA
* *** **
40318 AATT-ATATT-GTATAGTTTATAAACTAT-A
1 AATTAATATTAATATAAACTAT-AGTTATAA
* * *
40346 GACT-ATATTAATATAAATTATAGTTA-AGA
1 AATTAATATTAATATAAACTATAGTTATA-A
*
40375 TAATTAACATTAATATAAACTATAGTTTATAA
1 -AATTAATATTAATATAAACTATAG-TTATAA
40407 A
1 A
40408 TTATATACAA
Statistics
Matches: 93, Mismatches: 18, Indels: 18
0.72 0.14 0.14
Matches are distributed among these distances:
28 21 0.23
29 15 0.16
30 7 0.08
31 43 0.46
32 6 0.06
33 1 0.01
ACGTcount: A:0.50, C:0.04, G:0.05, T:0.41
Consensus pattern (30 bp):
AATTAATATTAATATAAACTATAGTTATAA
Found at i:40309 original size:24 final size:25
Alignment explanation
Indices: 40264--40310 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
40254 TGTAATTAAT
**
40264 ATTAATATAAAATATAGTCTATAAA
1 ATTAATATAAAATATAAACTATAAA
*
40289 ATTAATAT-TAATATAAACTATA
1 ATTAATATAAAATATAAACTATA
40311 TGTTATAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 11 0.58
25 8 0.42
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.38
Consensus pattern (25 bp):
ATTAATATAAAATATAAACTATAAA
Found at i:40332 original size:88 final size:88
Alignment explanation
Indices: 40262--40441 Score: 240
Period size: 88 Copynumber: 2.0 Consensus size: 88
40252 TTTGTAATTA
*
40262 ATATTAATATAAAATATAGTCTATA-A-AATTAATATTAATATAAACTATA-TGTTATAAATTAT
1 ATATTAATATAAAATATAGT-TA-AGATAATTAACATTAATATAAACTATAGT-TTATAAATTAT
40324 ATTGTATAGTTTATAAACTATAGACT
63 ATTGTATAGTTTATAAACTATAGACT
* *
40350 ATATTAATATAAATTATAGTTAAGATAATTAACATTAATATAAACTATAGTTTATAAATTATATA
1 ATATTAATATAAAATATAGTTAAGATAATTAACATTAATATAAACTATAGTTTATAAATTATATT
** * * *
40415 CAATAGGTTATAAAGTATAAACT
66 GTATAGTTTATAAACTATAGACT
40438 ATAT
1 ATAT
40442 AGTACACTAA
Statistics
Matches: 81, Mismatches: 8, Indels: 6
0.85 0.08 0.06
Matches are distributed among these distances:
86 1 0.01
87 3 0.04
88 76 0.94
89 1 0.01
ACGTcount: A:0.49, C:0.04, G:0.06, T:0.41
Consensus pattern (88 bp):
ATATTAATATAAAATATAGTTAAGATAATTAACATTAATATAAACTATAGTTTATAAATTATATT
GTATAGTTTATAAACTATAGACT
Found at i:40534 original size:57 final size:55
Alignment explanation
Indices: 40471--40606 Score: 157
Period size: 57 Copynumber: 2.4 Consensus size: 55
40461 TTGCTTATAA
* *
40471 ACTATAGGTTACATATATAGTTTATATA-ACTTATAAATATATTGTTTATATAAATAT
1 ACTATAGGTTACATATATAGTTTATATATAC-TATAAATA-ATT-TATACATAAATAT
* * * * * *
40528 ATTATAGGTTATATATATAGTTTATATATGCTATACATAGTTTATACATACATAT
1 ACTATAGGTTACATATATAGTTTATATATACTATAAATAATTTATACATAAATAT
*
40583 ACTATAAGTTACATATATAGTTTA
1 ACTATAGGTTACATATATAGTTTA
40607 CATGTATACA
Statistics
Matches: 67, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
55 31 0.46
56 2 0.03
57 33 0.49
58 1 0.01
ACGTcount: A:0.40, C:0.07, G:0.08, T:0.45
Consensus pattern (55 bp):
ACTATAGGTTACATATATAGTTTATATATACTATAAATAATTTATACATAAATAT
Found at i:40604 original size:35 final size:36
Alignment explanation
Indices: 40564--40637 Score: 96
Period size: 37 Copynumber: 2.1 Consensus size: 36
40554 TATGCTATAC
*
40564 ATAGTTT-ATACATACATATACTATAAGTTACATAT
1 ATAGTTTAATACATACATATACTATAAGTTACACAT
** *
40599 ATAGTTTACATGTATACATATACTATAGGTTACACAT
1 ATAGTTTA-ATACATACATATACTATAAGTTACACAT
40636 AT
1 AT
40638 TAACTATTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 7 0.21
37 26 0.79
ACGTcount: A:0.41, C:0.12, G:0.08, T:0.39
Consensus pattern (36 bp):
ATAGTTTAATACATACATATACTATAAGTTACACAT
Found at i:40772 original size:2 final size:2
Alignment explanation
Indices: 40765--41045 Score: 128
Period size: 2 Copynumber: 143.0 Consensus size: 2
40755 TTCTATAAAC
*
40765 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TC TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
40807 TA GA T- TA CT- TA TA TA GT- TA TA CA TA CA TA TA TA TA CTA TA
1 TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA
* * * *
40847 T- TA -A TA TA AA T- TA TA -A TT TA TA AA CTA TA TA T- TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
* * *
40885 TA T- TT TA TA CA TA TA TA GTT TA TA TA TA TA TA TA T- TA -A TA
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
40925 T- TA -A TA TA AA T- TA TA T- TT TA TA AA CTA TA TA CTT TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA
* * * * * *
40965 GTT TA TA CA TA TA TA GTT TA TA TA CA TA GTT TA TA TA TA TA GTT
1 -TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA TA TA TA TA TA -TA
*
41009 TA TA TA TA AA CT- TA TA T- 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
41046 ATTTTGTTTT
Statistics
Matches: 209, Mismatches: 41, Indels: 58
0.68 0.13 0.19
Matches are distributed among these distances:
1 17 0.08
2 180 0.86
3 12 0.06
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:40910 original size:17 final size:15
Alignment explanation
Indices: 40881--40917 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
40871 CTATATATTT
40881 TATATATTTTATACA
1 TATATATTTTATACA
* *
40896 TATATAGTTTATATA
1 TATATATTTTATACA
40911 TATATAT
1 TATATAT
40918 ATTAATATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (15 bp):
TATATATTTTATACA
Found at i:40987 original size:78 final size:77
Alignment explanation
Indices: 40833--40988 Score: 260
Period size: 78 Copynumber: 2.0 Consensus size: 77
40823 TTATACATAC
*
40833 ATATATATACTATATTAATATAAATTATAATTTATAAACTATATATTTTATATATTTTATACATA
1 ATATATATACTATATTAATATAAATTATAATTTATAAACTATATATTTTATATAGTTTATACATA
40898 TATAGTTTATAT
66 TATAGTTTATAT
* *
40910 ATATATATATTAATATTAATATAAATTATATTTTATAAACTATATACTTTT-TATAGTTTATACA
1 ATATATATACT-ATATTAATATAAATTATAATTTATAAACTATATA-TTTTATATAGTTTATACA
40974 TATATAGTTTATAT
64 TATATAGTTTATAT
40988 A
1 A
40989 CATAGTTTAT
Statistics
Matches: 74, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
77 10 0.14
78 60 0.81
79 4 0.05
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.51
Consensus pattern (77 bp):
ATATATATACTATATTAATATAAATTATAATTTATAAACTATATATTTTATATAGTTTATACATA
TATAGTTTATAT
Found at i:40993 original size:13 final size:13
Alignment explanation
Indices: 40961--41045 Score: 91
Period size: 13 Copynumber: 6.3 Consensus size: 13
40951 ATATACTTTT
40961 TATAGTTTATACATA
1 TATAGTTTAT--ATA
40976 TATAGTTTATATA
1 TATAGTTTATATA
*
40989 CATAGTTTATATA
1 TATAGTTTATATA
41002 TATAGTTTATATA
1 TATAGTTTATATA
* *
41015 TAAACTTATATTATA
1 TATAGTT-TA-TATA
*
41030 TATA-TATATATA
1 TATAGTTTATATA
41042 TATA
1 TATA
41046 ATTTTGTTTT
Statistics
Matches: 62, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
12 8 0.13
13 34 0.55
14 3 0.05
15 17 0.27
ACGTcount: A:0.42, C:0.04, G:0.05, T:0.49
Consensus pattern (13 bp):
TATAGTTTATATA
Found at i:41016 original size:17 final size:17
Alignment explanation
Indices: 40996--41042 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
40986 ATACATAGTT
40996 TATATATATAGT-TTATA
1 TATATATATA-TATTATA
*
41013 TATAAACT-TATATTATA
1 TATATA-TATATATTATA
41030 TATATATATATAT
1 TATATATATATAT
41043 ATAATTTTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
16 2 0.08
17 22 0.88
18 1 0.04
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (17 bp):
TATATATATATATTATA
Found at i:41024 original size:78 final size:77
Alignment explanation
Indices: 40816--40992 Score: 232
Period size: 78 Copynumber: 2.2 Consensus size: 77
40806 ATAGATTACT
* *
40816 TATATAGTTATACATACATATATA-TACTATATTAATATAAATTATAATTTATAAACTATATATT
1 TATATAGTT-TATATACATATATATTA--ATATT-ATATAAATTATAACTTATAAACTATATATT
*
40880 TTATATATTTTATACA
62 TTATATAGTTTATACA
* **
40896 TATATAGTTTATATATATATATATTAATATTAATATAAATTATATTTTATAAACTATATACTTTT
1 TATATAGTTTATATACATATATATTAATATT-ATATAAATTATAACTTATAAACTATATA-TTTT
40961 -TATAGTTTATACA
64 ATATAGTTTATACA
40974 TATATAGTTTATATACATA
1 TATATAGTTTATATACATA
40993 GTTTATATAT
Statistics
Matches: 90, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
78 63 0.70
79 16 0.18
80 11 0.12
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (77 bp):
TATATAGTTTATATACATATATATTAATATTATATAAATTATAACTTATAAACTATATATTTTAT
ATAGTTTATACA
Found at i:41142 original size:18 final size:18
Alignment explanation
Indices: 41119--41153 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
41109 AAACTATATA
41119 TATAGTTAATATGTAAAC
1 TATAGTTAATATGTAAAC
*
41137 TATAGTTCATATGTAAA
1 TATAGTTAATATGTAAA
41154 TTACATAGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.43, C:0.06, G:0.11, T:0.40
Consensus pattern (18 bp):
TATAGTTAATATGTAAAC
Found at i:41186 original size:14 final size:14
Alignment explanation
Indices: 41163--41206 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
41153 ATTACATAGG
* *
41163 TAAGAGTTAAGGTT
1 TAAGATTTAAAGTT
41177 TAAGATTTAAAGTT
1 TAAGATTTAAAGTT
* *
41191 TAGGATTTAGAGTT
1 TAAGATTTAAAGTT
41205 TA
1 TA
41207 GGGTATTAGG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.36, C:0.00, G:0.23, T:0.41
Consensus pattern (14 bp):
TAAGATTTAAAGTT
Found at i:41207 original size:14 final size:14
Alignment explanation
Indices: 41174--41222 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
41164 AAGAGTTAAG
* *
41174 GTTTAAGATTTAAA
1 GTTTAGGATTTAGA
41188 GTTTAGGATTTAGA
1 GTTTAGGATTTAGA
*
41202 GTTTAGGGTATTAG-
1 GTTTAGGAT-TTAGA
41216 GTTTAGG
1 GTTTAGG
41223 GTTATATAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
14 27 0.87
15 4 0.13
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.43
Consensus pattern (14 bp):
GTTTAGGATTTAGA
Found at i:41385 original size:42 final size:42
Alignment explanation
Indices: 41338--41447 Score: 193
Period size: 42 Copynumber: 2.6 Consensus size: 42
41328 TAGTTTATAC
*
41338 ATACATGTACTATAAGTTACATATATAGTTTACATTACATGT
1 ATACATATACTATAAGTTACATATATAGTTTACATTACATGT
*
41380 ATACATATACTATAAGTTACATATATAGTTTACATTGCATGT
1 ATACATATACTATAAGTTACATATATAGTTTACATTACATGT
*
41422 ATACACATACTATAAGTTACATATAT
1 ATACATATACTATAAGTTACATATAT
41448 TAACTATTGT
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 65 1.00
ACGTcount: A:0.40, C:0.13, G:0.08, T:0.39
Consensus pattern (42 bp):
ATACATATACTATAAGTTACATATATAGTTTACATTACATGT
Found at i:41659 original size:2 final size:2
Alignment explanation
Indices: 41654--41788 Score: 88
Period size: 2 Copynumber: 69.0 Consensus size: 2
41644 TGTTTTTTTA
*
41654 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T CT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
41695 AT -T AGT -T AT AC AT AC AT AT AT AT ACT AT AT -T A- AT AT AA AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT
* * * * *
41735 -T AT A- AC AT AT AA AT -T AT AT AGT TT AT AC AT AT AT AGT TT AT
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT A-T AT AT
41776 AT AT AT ACT AT AT
1 AT AT AT A-T AT AT
41789 TAATATAAAT
Statistics
Matches: 104, Mismatches: 16, Indels: 26
0.71 0.11 0.18
Matches are distributed among these distances:
1 8 0.08
2 89 0.86
3 7 0.07
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:41769 original size:15 final size:15
Alignment explanation
Indices: 41749--41782 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
41739 ACATATAAAT
41749 TATATAGTTTATACA
1 TATATAGTTTATACA
*
41764 TATATAGTTTATATA
1 TATATAGTTTATACA
41779 TATA
1 TATA
41783 CTATATTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (15 bp):
TATATAGTTTATACA
Found at i:41778 original size:17 final size:17
Alignment explanation
Indices: 41749--41818 Score: 60
Period size: 17 Copynumber: 4.4 Consensus size: 17
41739 ACATATAAAT
41749 TATATAG-TT-TATACA
1 TATATAGTTTATATACA
*
41764 TATATAGTTTATATATA
1 TATATAGTTTATATACA
* *
41781 TACTATA-TTAATATAAA
1 TA-TATAGTTTATATACA
*
41798 TA-ATAGTTTATAAAC-
1 TATATAGTTTATATACA
41813 TATATA
1 TATATA
41819 CTTTTTATAG
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
15 12 0.27
16 11 0.25
17 17 0.39
18 4 0.09
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (17 bp):
TATATAGTTTATATACA
Found at i:41779 original size:13 final size:13
Alignment explanation
Indices: 41749--41988 Score: 72
Period size: 13 Copynumber: 18.0 Consensus size: 13
41739 ACATATAAAT
41749 TATATAGTTTATACA
1 TATATAGTTTAT--A
41764 TATATAGTTTATA
1 TATATAGTTTATA
*
41777 TATATA--CTATA
1 TATATAGTTTATA
* *
41788 T-TA-A-TATAAA
1 TATATAGTTTATA
41798 TA-ATAGTTTATAAA
1 TATATAGTTTAT--A
*
41812 CTATATACTTT-T-
1 -TATATAGTTTATA
41824 T--ATAGTTTATACA
1 TATATAGTTTAT--A
*
41837 TATATAATTTATA
1 TATATAGTTTATA
*
41850 TATATAGTTCACATA
1 TATATAGTT--TATA
* * *
41865 AACATAATTTATA
1 TATATAGTTTATA
41878 TATATAGCTTATAATAA
1 TATATAG-TT-T-AT-A
41895 TAATATAGTTTATA
1 T-ATATAGTTTATA
**
41909 -ATATA-AATATA
1 TATATAGTTTATA
* *
41920 GTTTATAATTTTATA
1 -TATAT-AGTTTATA
*
41935 TACATAGTTTATA
1 TATATAGTTTATA
**
41948 TATATAGTGCACATA
1 TATATAGT--TTATA
* *
41963 AATATAATTTATA
1 TATATAGTTTATA
41976 TATATAGTTTATA
1 TATATAGTTTATA
41989 ATAATTATAT
Statistics
Matches: 164, Mismatches: 34, Indels: 56
0.65 0.13 0.22
Matches are distributed among these distances:
9 7 0.04
10 8 0.05
11 11 0.07
12 8 0.05
13 55 0.34
14 8 0.05
15 48 0.29
16 9 0.05
17 4 0.02
18 6 0.04
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (13 bp):
TATATAGTTTATA
Found at i:41841 original size:64 final size:63
Alignment explanation
Indices: 41700--41842 Score: 151
Period size: 64 Copynumber: 2.2 Consensus size: 63
41690 TATATATTAG
* * *
41700 TTATACATACATATATATACTATATTAATATAAATTATAACATATAAATTATATAGTTTATACAT
1 TTATACAT--ATATATATACTATATTAATATAAATAATAACATATAAACTATATACTTTATACAT
* ** *** * *
41765 ATATAGTTTATATATATACTATATTAATATAAATAATAGTTTATAAACTATATACTTTTTATAGT
1 TTATA-CATATATATATACTATATTAATATAAATAATAACATATAAACTATATACTTTATACA-T
41830 TTATACATATATA
1 TTATACATATATA
41843 ATTTATATAT
Statistics
Matches: 62, Mismatches: 14, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
64 52 0.84
65 9 0.15
66 1 0.02
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.45
Consensus pattern (63 bp):
TTATACATATATATATACTATATTAATATAAATAATAACATATAAACTATATACTTTATACAT
Found at i:41902 original size:18 final size:18
Alignment explanation
Indices: 41874--42029 Score: 95
Period size: 18 Copynumber: 8.3 Consensus size: 18
41864 AAACATAATT
* *
41874 TATATATATAGCTTATAA
1 TATAAATATAGTTTATAA
41892 TA-ATAATATAGTTTATAA
1 TATA-AATATAGTTTATAA
41910 TATAAATATAGTTTATAA
1 TATAAATATAGTTTATAA
* *
41928 TTTTATATACATAGTTTATATA
1 ---TATAAATATAGTTTATA-A
* * **
41950 TATAGTGCACATA-AATATAA
1 TATA---AATATAGTTTATAA
*
41970 TTTATATATATAGTTTATAA
1 --TATAAATATAGTTTATAA
*
41990 TA-ATTATATAGTTTATAA
1 TATA-AATATAGTTTATAA
42008 TATAAATATAGTTTAT-A
1 TATAAATATAGTTTATAA
42025 TATAA
1 TATAA
42030 TTTTTTATTA
Statistics
Matches: 112, Mismatches: 12, Indels: 29
0.73 0.08 0.19
Matches are distributed among these distances:
17 8 0.07
18 59 0.53
19 10 0.09
20 6 0.05
21 19 0.17
22 10 0.09
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.46
Consensus pattern (18 bp):
TATAAATATAGTTTATAA
Found at i:41970 original size:98 final size:99
Alignment explanation
Indices: 41765--42024 Score: 332
Period size: 98 Copynumber: 2.6 Consensus size: 99
41755 GTTTATACAT
* * *
41765 ATATAGTTTATATATATA-CTATATTAAT-ATAAATAATAGTTTATAA-ACTATATACT-TTTTA
1 ATATAATTTATATATATAGCT-TA-TAATAAT-AAT-ATAGTTTATAATA-TAAATA-TAGTTTA
* * *
41826 TAGTTTATACATATATAATTTATATATATAGTTCACATAA
60 TAATTTATACATACATAATTTATATATATAGTGCACATAA
*
41866 ACATAATTTATATATATAGCTTATAATAATAATATAGTTTATAATATAAATATAGTTTATAATTT
1 ATATAATTTATATATATAGCTTATAATAATAATATAGTTTATAATATAAATATAGTTTATAATTT
* *
41931 -TATATACATAGTTTATATATATAGTGCACATAA
66 ATACATACATAATTTATATATATAGTGCACATAA
* *
41964 ATATAATTTATATATATAGTTTATAATAATTATATAGTTTATAATATAAATATAGTTTATA
1 ATATAATTTATATATATAGCTTATAATAATAATATAGTTTATAATATAAATATAGTTTATA
42025 TATAATTTTT
Statistics
Matches: 143, Mismatches: 12, Indels: 11
0.86 0.07 0.07
Matches are distributed among these distances:
98 88 0.62
99 25 0.17
100 8 0.06
101 20 0.14
102 2 0.01
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.46
Consensus pattern (99 bp):
ATATAATTTATATATATAGCTTATAATAATAATATAGTTTATAATATAAATATAGTTTATAATTT
ATACATACATAATTTATATATATAGTGCACATAA
Found at i:42847 original size:64 final size:64
Alignment explanation
Indices: 42709--42847 Score: 181
Period size: 64 Copynumber: 2.2 Consensus size: 64
42699 GAACTGAAAA
* *
42709 TTACCCGACCTGAACTCGATCTGGATCTGGTGTCAAATCAACCTTAAAATAACCCGAACTGATT
1 TTACCCGACCTGAACCCGATCTGGATCTGGTGTCAAATCAACCTTAAAATAACCCGAACCGATT
* * * * ** *
42773 TGACCTGACCTGAACCCGATCTGGATCTGGTGTCAAATCAACC-TAAATTGACTTGTACCCGATT
1 TTACCCGACCTGAACCCGATCTGGATCTGGTGTCAAATCAACCTTAAAATAACCCG-AACCGATT
42837 TTACCCGACCT
1 TTACCCGACCT
42848 ACCAAGATCC
Statistics
Matches: 63, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
63 8 0.13
64 55 0.87
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.27
Consensus pattern (64 bp):
TTACCCGACCTGAACCCGATCTGGATCTGGTGTCAAATCAACCTTAAAATAACCCGAACCGATT
Found at i:43647 original size:2 final size:2
Alignment explanation
Indices: 43640--43665 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
43630 TAAGCCATAA
43640 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
43666 TCTTTTTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:51461 original size:36 final size:36
Alignment explanation
Indices: 51417--51488 Score: 92
Period size: 37 Copynumber: 2.0 Consensus size: 36
51407 TGGCAACCAA
* *
51417 CTTTG-AAAAATGTTTTTCAAAGTGTGGTAAATGTTT
1 CTTTGAAAAAATATTTTTCAAAATGTGGTAAA-GTTT
* *
51453 CTTTGAAAAAATATTTTTTAAAATTTGGTAAAGTTT
1 CTTTGAAAAAATATTTTTCAAAATGTGGTAAAGTTT
51489 GGTAGATGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 9 0.29
37 22 0.71
ACGTcount: A:0.35, C:0.04, G:0.15, T:0.46
Consensus pattern (36 bp):
CTTTGAAAAAATATTTTTCAAAATGTGGTAAAGTTT
Found at i:51923 original size:16 final size:16
Alignment explanation
Indices: 51902--51950 Score: 89
Period size: 16 Copynumber: 3.0 Consensus size: 16
51892 TTAATATTCA
51902 CGTGAATAGTAAATTT
1 CGTGAATAGTAAATTT
51918 CGTGAATAGTAAATTT
1 CGTGAATAGTAAATTT
51934 CGTGAATAGTGAAATTT
1 CGTGAATAGT-AAATTT
51951 TGTCGGCGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
16 26 0.81
17 6 0.19
ACGTcount: A:0.37, C:0.06, G:0.20, T:0.37
Consensus pattern (16 bp):
CGTGAATAGTAAATTT
Found at i:56055 original size:37 final size:37
Alignment explanation
Indices: 55997--56077 Score: 112
Period size: 37 Copynumber: 2.2 Consensus size: 37
55987 TAGCAACCAA
*
55997 CTTTG-AAAAATGTTTTCCAAAATTTGGTAAATGTTT
1 CTTTGAAAAAATATTTTCCAAAATTTGGTAAATGTTT
* *
56033 CTTTGAAAAAATATTTTTCAAAATTTGGTAGATGTTT
1 CTTTGAAAAAATATTTTCCAAAATTTGGTAAATGTTT
*
56070 -GTTGAAAA
1 CTTTGAAAA
56078 TAGGAATGAG
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
36 12 0.30
37 28 0.70
ACGTcount: A:0.36, C:0.06, G:0.15, T:0.43
Consensus pattern (37 bp):
CTTTGAAAAAATATTTTCCAAAATTTGGTAAATGTTT
Found at i:58620 original size:31 final size:31
Alignment explanation
Indices: 58559--58624 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 31
58549 TTGATAATTC
* * *
58559 TATAA-AATTTTGAGTTTTTTTTAAACAAAT
1 TATAATAATTTTGAATTTTTTTAAAAAAAAT
58589 TATAATAATTTT-AATTTTTTTAAATAAAAAT
1 TATAATAATTTTGAATTTTTTTAAA-AAAAAT
58620 T-TAAT
1 TATAAT
58625 TTTTTTAAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
30 19 0.61
31 12 0.39
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.52
Consensus pattern (31 bp):
TATAATAATTTTGAATTTTTTTAAAAAAAAT
Found at i:59229 original size:18 final size:18
Alignment explanation
Indices: 59206--59287 Score: 55
Period size: 21 Copynumber: 4.5 Consensus size: 18
59196 ATTTGTCCCC
59206 TATATATATATTTTTAA-
1 TATATATATATTTTTAAT
*
59223 T-TATATAT-TTTTTATT
1 TATATATATATTTTTAAT
* * *
59239 TACTATATTCCTTTTTTTATT
1 TA-TATA-T-ATATTTTTAAT
59260 TATAT-TATATTATTTATAT
1 TATATATATATT-TTTA-AT
59279 TATATATAT
1 TATATATAT
59288 CTTATATCAT
Statistics
Matches: 51, Mismatches: 5, Indels: 15
0.72 0.07 0.21
Matches are distributed among these distances:
15 6 0.12
16 8 0.16
17 4 0.08
18 9 0.18
19 7 0.14
20 7 0.14
21 10 0.20
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.65
Consensus pattern (18 bp):
TATATATATATTTTTAAT
Found at i:59274 original size:14 final size:14
Alignment explanation
Indices: 59255--59294 Score: 62
Period size: 14 Copynumber: 2.7 Consensus size: 14
59245 ATTCCTTTTT
59255 TTATTTATATTATA
1 TTATTTATATTATA
59269 TTATTTATATTATA
1 TTATTTATATTATA
59283 TATATCTTATAT
1 T-TAT-TTATAT
59295 CATTATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 15 0.62
15 3 0.12
16 6 0.25
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (14 bp):
TTATTTATATTATA
Found at i:59466 original size:13 final size:13
Alignment explanation
Indices: 59448--59472 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
59438 TTACTTTATT
59448 TTATTTTTTTCTA
1 TTATTTTTTTCTA
59461 TTATTTTTTTCT
1 TTATTTTTTTCT
59473 TAATATCATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.08, G:0.00, T:0.80
Consensus pattern (13 bp):
TTATTTTTTTCTA
Found at i:59536 original size:35 final size:36
Alignment explanation
Indices: 59461--59541 Score: 105
Period size: 35 Copynumber: 2.3 Consensus size: 36
59451 TTTTTTTCTA
*
59461 TTATTT-TTTT-CTTAATATCATGTATATATTATTT
1 TTATTTGTTTTACTTAATATCATATATATATTATTT
* * *
59495 TTATTTGTTTTACTTAGTATTATATATTTATTA-TT
1 TTATTTGTTTTACTTAATATCATATATATATTATTT
59530 TTATTTGTTTTA
1 TTATTTGTTTTA
59542 ATAAATACTA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
34 6 0.15
35 18 0.44
36 17 0.41
ACGTcount: A:0.25, C:0.04, G:0.05, T:0.67
Consensus pattern (36 bp):
TTATTTGTTTTACTTAATATCATATATATATTATTT
Found at i:59732 original size:26 final size:27
Alignment explanation
Indices: 59673--59738 Score: 68
Period size: 26 Copynumber: 2.5 Consensus size: 27
59663 ATTCATTTTG
59673 TTTATTT-TTTAT-TATTTTTTACATGT
1 TTTATTTATTT-TCTATTTTTTACATGT
* *
59699 TTT-GTTATTTTCTATTTTTT-CTTGT
1 TTTATTTATTTTCTATTTTTTACATGT
59724 TTTATTTATTATTCT
1 TTTATTTATT-TTCT
59739 CACATTTTCA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
25 10 0.30
26 19 0.58
27 4 0.12
ACGTcount: A:0.15, C:0.06, G:0.05, T:0.74
Consensus pattern (27 bp):
TTTATTTATTTTCTATTTTTTACATGT
Found at i:62883 original size:14 final size:13
Alignment explanation
Indices: 62860--62912 Score: 67
Period size: 13 Copynumber: 4.2 Consensus size: 13
62850 ATAAAAAGAG
62860 AAAA-AAAGAGAA
1 AAAACAAAGAGAA
62872 AAAAGCAAAGAGAA
1 AAAA-CAAAGAGAA
62886 AATAA-AAAGAGAA
1 AA-AACAAAGAGAA
62899 AAAACAAAG-GAA
1 AAAACAAAGAGAA
62911 AA
1 AA
62913 TTGAAGAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
12 11 0.30
13 14 0.38
14 10 0.27
15 2 0.05
ACGTcount: A:0.77, C:0.04, G:0.17, T:0.02
Consensus pattern (13 bp):
AAAACAAAGAGAA
Found at i:62898 original size:27 final size:25
Alignment explanation
Indices: 62862--62913 Score: 86
Period size: 27 Copynumber: 2.0 Consensus size: 25
62852 AAAAAGAGAA
62862 AAAAAGAGAAAAAAGCAAAGAGAAAAT
1 AAAAAGAGAAAAAA-CAAAG-GAAAAT
62889 AAAAAGAGAAAAAACAAAGGAAAAT
1 AAAAAGAGAAAAAACAAAGGAAAAT
62914 TGAAGAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 6 0.24
26 5 0.20
27 14 0.56
ACGTcount: A:0.75, C:0.04, G:0.17, T:0.04
Consensus pattern (25 bp):
AAAAAGAGAAAAAACAAAGGAAAAT
Found at i:62900 original size:26 final size:25
Alignment explanation
Indices: 62854--62913 Score: 79
Period size: 25 Copynumber: 2.4 Consensus size: 25
62844 ATTAGAATAA
* *
62854 AAAGAGAAAA-AAAGAGAAAAAAGC
1 AAAGAGAAAATAAAAAGAAAAAAAC
62878 AAAGAGAAAATAAAAAGAGAAAAAAC
1 AAAGAGAAAATAAAAAGA-AAAAAAC
62904 AAAG-GAAAAT
1 AAAGAGAAAAT
62914 TGAAGAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
24 10 0.31
25 12 0.38
26 10 0.31
ACGTcount: A:0.75, C:0.03, G:0.18, T:0.03
Consensus pattern (25 bp):
AAAGAGAAAATAAAAAGAAAAAAAC
Found at i:63103 original size:69 final size:69
Alignment explanation
Indices: 62985--63113 Score: 231
Period size: 69 Copynumber: 1.9 Consensus size: 69
62975 GATTCAAACT
*
62985 ATGAGATTGATCAAGCACAATCATTTCCGAATCACTGAACCACTTCACTCGAAGATCATAAAACA
1 ATGAGATTGATCAAGCACAATCATTTCCGAATCACTGAACCACTCCACTCGAAGATCATAAAACA
63050 TCAA
66 TCAA
* *
63054 ATGAGATTGATCAAGCACAATCATTTCTGAATCACTGAATCACTCCACTCGAAGATCATA
1 ATGAGATTGATCAAGCACAATCATTTCCGAATCACTGAACCACTCCACTCGAAGATCATA
63114 GAGCATTAAG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
69 57 1.00
ACGTcount: A:0.39, C:0.24, G:0.12, T:0.25
Consensus pattern (69 bp):
ATGAGATTGATCAAGCACAATCATTTCCGAATCACTGAACCACTCCACTCGAAGATCATAAAACA
TCAA
Found at i:64624 original size:39 final size:39
Alignment explanation
Indices: 64581--64672 Score: 94
Period size: 39 Copynumber: 2.3 Consensus size: 39
64571 ACTGTTTTTA
* * *
64581 AAACAGAAGATTTTATCTCGCTTGAGATAGTTTCCCTTG
1 AAACAAAAGATTGTATCTCGCTTGAGACAGTTTCCCTTG
* * * **
64620 AAACAAAATATTGTCTCTCTCTTGAGACAGTTTCTTTTG
1 AAACAAAAGATTGTATCTCGCTTGAGACAGTTTCCCTTG
*
64659 AAACATAAACATTG
1 AAACA-AAAGATTG
64673 AAAACATTTC
Statistics
Matches: 43, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
39 36 0.84
40 7 0.16
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (39 bp):
AAACAAAAGATTGTATCTCGCTTGAGACAGTTTCCCTTG
Found at i:64726 original size:36 final size:36
Alignment explanation
Indices: 64679--64765 Score: 93
Period size: 37 Copynumber: 2.4 Consensus size: 36
64669 ATTGAAAACA
* * *
64679 TTTCCCTTGAAACGAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
* * *
64715 TTTCCCTTGAAATAAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAA-CAAATTTCGTCTCTCTTGAGACAG
* *
64752 TTTCTCTTTAAACA
1 TTTCCCTTGAAACA
64766 TAAACATTAA
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
36 13 0.30
37 30 0.70
ACGTcount: A:0.25, C:0.21, G:0.13, T:0.41
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
Found at i:64746 original size:37 final size:36
Alignment explanation
Indices: 64679--64755 Score: 109
Period size: 37 Copynumber: 2.1 Consensus size: 36
64669 ATTGAAAACA
** * *
64679 TTTCCCTTGAAACGAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAAAAAATTTTGTCTCCCTTGAGACAG
64715 TTTCCCTTGAAATAAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAA-AAAATTTTGTCTCCCTTGAGACAG
64752 TTTC
1 TTTC
64756 TCTTTAAACA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
36 12 0.33
37 24 0.67
ACGTcount: A:0.23, C:0.21, G:0.14, T:0.42
Consensus pattern (36 bp):
TTTCCCTTGAAAAAAATTTTGTCTCCCTTGAGACAG
Found at i:64790 original size:102 final size:101
Alignment explanation
Indices: 64590--64861 Score: 393
Period size: 102 Copynumber: 2.7 Consensus size: 101
64580 AAAACAGAAG
* *
64590 ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACAAAATATTGTCTCTCTCTTGAGACAGTTTCT
1 ATTTTATCTCTCTTGAGATAGTTTCCCTTGAAA-AAAATTTTGTCTC-C-CTTGAGACAGTTTCT
* *
64655 TTTGAAACATAAACATTGAAAACATTTCCCTTGAAACGA
63 TTTGAAACATAAACATTAAAAACATTTCCCTTGAAACAA
*
64694 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAATAAAATTTTGTCTCCCTTGAGACAGTTTCTCT
1 ATTTTATCTCTCTTGAGATAGTTTCCCTTGAAA-AAAATTTTGTCTCCCTTGAGACAGTTTCT-T
*
64759 TT-AAACATAAACATTAAAAACATTTCCCTTGAAATAA
64 TTGAAACATAAACATTAAAAACATTTCCCTTGAAACAA
* * * * *
64796 AGTTCATCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTT
1 ATTTTATCTCTCTTGAGATAGTTTCCCTTGAAAAAAATTTTGTCTCCCTTGAGACAGTTTCTTTT
64861 G
66 G
64862 GAACTAAGTT
Statistics
Matches: 153, Mismatches: 13, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
100 3 0.02
101 27 0.18
102 76 0.50
103 4 0.03
104 43 0.28
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.38
Consensus pattern (101 bp):
ATTTTATCTCTCTTGAGATAGTTTCCCTTGAAAAAAATTTTGTCTCCCTTGAGACAGTTTCTTTT
GAAACATAAACATTAAAAACATTTCCCTTGAAACAA
Found at i:64887 original size:37 final size:36
Alignment explanation
Indices: 64781--64937 Score: 206
Period size: 36 Copynumber: 4.3 Consensus size: 36
64771 ATTAAAAACA
* * * *
64781 TTTCCCTTGAAATAAAGTTCATCTCTCTTGAGACAG
1 TTTCTCTTGAAACAAATTTCGTCTCTCTTGAGACAG
* *
64817 TTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACAG
1 TTTCTCTTGAAACAAATTTCGTCTCTCTTGAGACAG
* * * *
64853 TTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAG
1 TTTCTCTTGAAAC-AAATTTCGTCTCTCTTGAGACAG
64890 TTTCTCTTGAAACAAATTTCGTCTCTCTTGAGACAG
1 TTTCTCTTGAAACAAATTTCGTCTCTCTTGAGACAG
*
64926 TTTCCCTTGAAA
1 TTTCTCTTGAAA
64938 TAAAATCTTT
Statistics
Matches: 105, Mismatches: 15, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
36 74 0.70
37 31 0.30
ACGTcount: A:0.24, C:0.22, G:0.15, T:0.39
Consensus pattern (36 bp):
TTTCTCTTGAAACAAATTTCGTCTCTCTTGAGACAG
Found at i:65069 original size:67 final size:67
Alignment explanation
Indices: 64899--65071 Score: 219
Period size: 67 Copynumber: 2.6 Consensus size: 67
64889 GTTTCTCTTG
* * * * * *
64899 AAACAAATTTCGTCTCTCTTGAGACAGTTTCCCTTG-AA-ATAAAATCTTTAAATTTATTTCCCC
1 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCATGAAACACAAAATCTTCAAATTTATTTCCCC
64962 TA
66 TA
* *
64964 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAATTTATTTCCCT
1 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCATGAAACACAAAATCTTCAAATTTATTTCCCC
65029 TA
66 TA
*
65031 AAACAAAATTTTGTTTCCCTTGAGATC-GTTT-TCATGAAACA
1 AAAC-AAATTTTGTCTCCCTTGAGA-CAGTTTCTCATGAAACA
65072 ACATATATCT
Statistics
Matches: 96, Mismatches: 8, Indels: 6
0.87 0.07 0.05
Matches are distributed among these distances:
65 33 0.34
66 2 0.02
67 37 0.39
68 23 0.24
69 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.09, T:0.38
Consensus pattern (67 bp):
AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCATGAAACACAAAATCTTCAAATTTATTTCCCC
TA
Found at i:65938 original size:106 final size:105
Alignment explanation
Indices: 65745--66227 Score: 512
Period size: 106 Copynumber: 4.6 Consensus size: 105
65735 ATATCGTGCC
* * * *
65745 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCATCAAACAATTTCCC
1 ACTCAAGACAACACAAGCTCAACTTCACAACGAAGGGACGGCTGATTGTCAACAAACAATTT-CC
* * *
65810 AGTTTCAGAA-CCAATTTTAACTTCACAGCGAAGGATATTGG
65 AATTTCA-AAGCCAATTTCAACTTCACAGCAAAGGATATTGG
* ** * *
65851 ATTCAAGACAACACAAATTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAACTTTCC
1 ACTCAAGACAACACAAGCTCAACTTCACAACGAAGGGACGGCTGATTGTCAACAAACAA-TTTCC
*
65916 AATTTCAAAGCCAATTTCAACTTCACAGCAAATGATATTGG
65 AATTTCAAAGCCAATTTCAACTTCACAGCAAAGGATATTGG
* * * ** *
65957 ACTCAAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGATTGATTGTCAACAAACAACTTCCC
1 ACTCAAGACAACACAAGCTCAACTTCACAACGAAGGGACGGCTGATTGTCAACAAACAA-TTTCC
** * * *
66022 AATTTCAGGGCCAATTTTAACTTCCCAGCGAAGGATATTGG
65 AATTTCAAAGCCAATTTCAACTTCACAGCAAAGGATATTGG
* * * * *
66063 ACCCAAGACAACACAAGATCAACTTCACGACGAAGGGGA-GGCTGATTATCGAC-AA-AATTT-C
1 ACTCAAGACAACACAAGCTCAACTTCACAACGAA-GGGACGGCTGATTGTCAACAAACAATTTCC
* * * * *
66124 -A-TTCAGAGTCAATTTCAACTTTACAACAAAGGATATTAG
65 AATTTCAAAGCCAATTTCAACTTCACAGCAAAGGATATTGG
* * ** * *
66163 ACTCGAGACAGCACAAGCTCAACTTCACAGTGAAGGGGCGGCTGACTGTCAACAAACAATTTCCA
1 ACTCAAGACAACACAAGCTCAACTTCACAACGAAGGGACGGCTGATTGTCAACAAACAATTTCCA
66228 GAGCCAATTT
Statistics
Matches: 315, Mismatches: 54, Indels: 18
0.81 0.14 0.05
Matches are distributed among these distances:
99 3 0.01
100 68 0.22
101 3 0.01
102 6 0.02
103 3 0.01
104 2 0.01
105 4 0.01
106 220 0.70
107 6 0.02
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.22
Consensus pattern (105 bp):
ACTCAAGACAACACAAGCTCAACTTCACAACGAAGGGACGGCTGATTGTCAACAAACAATTTCCA
ATTTCAAAGCCAATTTCAACTTCACAGCAAAGGATATTGG
Found at i:66042 original size:212 final size:206
Alignment explanation
Indices: 65745--66226 Score: 617
Period size: 212 Copynumber: 2.3 Consensus size: 206
65735 ATATCGTGCC
* * * * * *
65745 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCATCAAACAATTTCCC
1 ACTCGAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGGCTGATTGTCAACAAACAATTTCCC
* **
65810 AGTTTCAGAACCAATTTTAACTTCACAGCGAAGGATATTGGATTCAAGACAACACAA-ATTCAAC
66 AATTTCAGAACCAATTTTAACTTCACAGCGAAGGATATTGGACCCAAGACAACACAAGA-TCAAC
* *
65874 TTCACAACGAA-GGGACGACTGGTTGTCAACAAACAACTTTCCAATTTCAAAGCCAATTTCAACT
130 TTCACAACGAAGGGGA-GACTGATTATCAAC-AA-AA-TTT-C-A-TTCAAAGCCAATTTCAACT
* * *
65938 TCACAGCAAATGATATTGG
188 TCACAACAAAGGATATTAG
* ** *
65957 ACTCAAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGATTGATTGTCAACAAACAACTTCCC
1 ACTCGAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGGCTGATTGTCAACAAACAATTTCCC
** *
66022 AATTTCAGGGCCAATTTTAACTTCCCAGCGAAGGATATTGGACCCAAGACAACACAAGATCAACT
66 AATTTCAGAACCAATTTTAACTTCACAGCGAAGGATATTGGACCCAAGACAACACAAGATCAACT
* * * * * *
66087 TCACGACGAAGGGGAGGCTGATTATCGACAAAATTTCATTCAGAGTCAATTTCAACTTTACAACA
131 TCACAACGAAGGGGAGACTGATTATCAACAAAATTTCATTCAAAGCCAATTTCAACTTCACAACA
66152 AAGGATATTAG
196 AAGGATATTAG
* *
66163 ACTCGAGACAGCACAAGCTCAACTTCACAGTGAAGGGGCGGCTGACTGTCAACAAACAATTTCC
1 ACTCGAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGGCTGATTGTCAACAAACAATTTCC
66227 AGAGCCAATT
Statistics
Matches: 235, Mismatches: 33, Indels: 10
0.85 0.12 0.04
Matches are distributed among these distances:
206 90 0.38
207 1 0.00
208 1 0.00
209 3 0.01
210 2 0.01
211 2 0.01
212 131 0.56
213 5 0.02
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.22
Consensus pattern (206 bp):
ACTCGAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGGCTGATTGTCAACAAACAATTTCCC
AATTTCAGAACCAATTTTAACTTCACAGCGAAGGATATTGGACCCAAGACAACACAAGATCAACT
TCACAACGAAGGGGAGACTGATTATCAACAAAATTTCATTCAAAGCCAATTTCAACTTCACAACA
AAGGATATTAG
Found at i:67615 original size:23 final size:22
Alignment explanation
Indices: 67587--67629 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
67577 TTAATTATAT
*
67587 TTTTTATTTATTTACTATATTCC
1 TTTTTATTTATATA-TATATTCC
67610 TTTTTATTTATATATATATT
1 TTTTTATTTATATATATATT
67630 TTTATTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (22 bp):
TTTTTATTTATATATATATTCC
Found at i:67625 original size:2 final size:2
Alignment explanation
Indices: 67618--67692 Score: 66
Period size: 2 Copynumber: 38.5 Consensus size: 2
67608 CCTTTTTATT
* * *
67618 TA TA TA TA TA TT TT TA T- TA TA TA TA TC T- TA TA TCA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA
* * *
67658 TA TA TA TA TA TA TA TA TA TA TG TA TG TA GA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
67693 TAATTTTCTC
Statistics
Matches: 60, Mismatches: 9, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
1 3 0.05
2 55 0.92
3 2 0.03
ACGTcount: A:0.40, C:0.03, G:0.04, T:0.53
Consensus pattern (2 bp):
TA
Found at i:67741 original size:18 final size:18
Alignment explanation
Indices: 67718--67782 Score: 67
Period size: 18 Copynumber: 3.5 Consensus size: 18
67708 ACTATGTATA
67718 TATATTTTTTCTTAATAT
1 TATATTTTTTCTTAATAT
* * **
67736 TATATTTATACGTTTTTAT
1 TATATTTTTTC-TTAATAT
67755 ATATATTTTTTCTTAATAT
1 -TATATTTTTTCTTAATAT
*
67774 TCTATTTTT
1 TATATTTTT
67783 GTTATTTATT
Statistics
Matches: 36, Mismatches: 9, Indels: 4
0.73 0.18 0.08
Matches are distributed among these distances:
18 17 0.47
19 10 0.28
20 9 0.25
ACGTcount: A:0.26, C:0.06, G:0.02, T:0.66
Consensus pattern (18 bp):
TATATTTTTTCTTAATAT
Found at i:67823 original size:16 final size:17
Alignment explanation
Indices: 67787--67871 Score: 56
Period size: 16 Copynumber: 5.2 Consensus size: 17
67777 ATTTTTGTTA
*
67787 TTTATTTATA-TA-TAT
1 TTTATTTTTACTATTAT
*
67802 TATATTTTTACT-TTAT
1 TTTATTTTTACTATTAT
*
67818 TTTATTTTTTCTATTAT
1 TTTATTTTTACTATTAT
* *
67835 TTT-TTTCTTAATATCAT
1 TTTATTT-TTACTATTAT
*
67852 GTATATTTTTA-T-TTAT
1 -TTTATTTTTACTATTAT
67868 TTTA
1 TTTA
67872 CTTAGTATTA
Statistics
Matches: 54, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
15 11 0.20
16 20 0.37
17 15 0.28
18 5 0.09
19 3 0.06
ACGTcount: A:0.25, C:0.05, G:0.01, T:0.69
Consensus pattern (17 bp):
TTTATTTTTACTATTAT
Found at i:67827 original size:75 final size:75
Alignment explanation
Indices: 67748--67901 Score: 181
Period size: 75 Copynumber: 2.0 Consensus size: 75
67738 TATTTATACG
* *
67748 TTTTTATA-TATATTTTTTCTTAATAT-TCTATTTTTGTTATTTATTTATA-TA-TATTATATTT
1 TTTTTATATTAT-TTTTTTCTTAATATATCTATATTT-TTATTTATTT-TACTAGTATTATATAT
*
67809 TTACTTTATTTTAT
63 TTACTAT-TTTTAT
* *
67823 TTTTTCTATTATTTTTTTCTTAATATCATGTATATTTTTATTTATTTTACTTAGTATTATATATT
1 TTTTTATATTATTTTTTTCTTAATAT-ATCTATATTTTTATTTATTTTAC-TAGTATTATATATT
67888 TACTATTTTTAT
64 TACTATTTTTAT
67900 TT
1 TT
67902 GTTTTAGTAA
Statistics
Matches: 68, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
75 23 0.34
76 13 0.19
77 17 0.25
78 15 0.22
ACGTcount: A:0.25, C:0.05, G:0.02, T:0.68
Consensus pattern (75 bp):
TTTTTATATTATTTTTTTCTTAATATATCTATATTTTTATTTATTTTACTAGTATTATATATTTA
CTATTTTTAT
Found at i:68109 original size:27 final size:27
Alignment explanation
Indices: 68050--68102 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
68040 TATTTTATTA
*
68050 TTATTTTTATTATTTTTTACGTGTTTTG
1 TTATTTTT-CTATTTTTTACGTGTTTTG
*
68078 TTATTTTTCTATTTTTT-CTTGTTTT
1 TTATTTTTCTATTTTTTACGTGTTTT
68103 ATTTATTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 7 0.30
27 8 0.35
28 8 0.35
ACGTcount: A:0.11, C:0.06, G:0.08, T:0.75
Consensus pattern (27 bp):
TTATTTTTCTATTTTTTACGTGTTTTG
Found at i:68114 original size:27 final size:27
Alignment explanation
Indices: 68060--68114 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
68050 TTATTTTTAT
*
68060 TATTTTTTACGTGTTTTGTTATTTTTC
1 TATTTTTTACGTGTTTTGTTATTATTC
* *
68087 TATTTTTT-CTTGTTTTATTTATTATTC
1 TATTTTTTACGTGTTTT-GTTATTATTC
68114 T
1 T
68115 CACATTTTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 7 0.29
27 17 0.71
ACGTcount: A:0.13, C:0.07, G:0.07, T:0.73
Consensus pattern (27 bp):
TATTTTTTACGTGTTTTGTTATTATTC
Found at i:70671 original size:75 final size:75
Alignment explanation
Indices: 70548--70700 Score: 306
Period size: 75 Copynumber: 2.0 Consensus size: 75
70538 GGAGGTTGAA
70548 CAAGGAGATTCTTCTGAAGCAGAACCAGCACATGATGAACAAGAACCAGAGAGTTCTGAAGCTCC
1 CAAGGAGATTCTTCTGAAGCAGAACCAGCACATGATGAACAAGAACCAGAGAGTTCTGAAGCTCC
70613 AAGAACTCGT
66 AAGAACTCGT
70623 CAAGGAGATTCTTCTGAAGCAGAACCAGCACATGATGAACAAGAACCAGAGAGTTCTGAAGCTCC
1 CAAGGAGATTCTTCTGAAGCAGAACCAGCACATGATGAACAAGAACCAGAGAGTTCTGAAGCTCC
70688 AAGAACTCGT
66 AAGAACTCGT
70698 CAA
1 CAA
70701 TCAGATCGTG
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 78 1.00
ACGTcount: A:0.38, C:0.23, G:0.22, T:0.17
Consensus pattern (75 bp):
CAAGGAGATTCTTCTGAAGCAGAACCAGCACATGATGAACAAGAACCAGAGAGTTCTGAAGCTCC
AAGAACTCGT
Found at i:72416 original size:20 final size:21
Alignment explanation
Indices: 72379--72420 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
72369 GTCATGCAAT
72379 TAATAATAGTTGCATAATGCA
1 TAATAATAGTTGCATAATGCA
*
72400 TAATAATGGTT-CATAATGCA
1 TAATAATAGTTGCATAATGCA
72420 T
1 T
72421 TGTAAGTTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (21 bp):
TAATAATAGTTGCATAATGCA
Done.