Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397257.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_95.0, 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: 12062019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 103452 characters in sequence are not A, C, G, or T
File 26 of 26
Found at i:11709825 original size:20 final size:20
Alignment explanation
Indices: 11709800--11709838 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
11709790 GCCCCCGCTC
11709800 CTCCATCGAT-CTCATCACAT
1 CTCCATCGATACT-ATCACAT
*
11709820 CTCCATGGATACTATCACA
1 CTCCATCGATACTATCACA
11709839 GTGGTTCAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.28, C:0.36, G:0.08, T:0.28
Consensus pattern (20 bp):
CTCCATCGATACTATCACAT
Found at i:11711126 original size:2 final size:2
Alignment explanation
Indices: 11711119--11711144 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
11711109 AATGACAACT
11711119 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
11711145 ATTAATTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:11715448 original size:2 final size:2
Alignment explanation
Indices: 11715443--11715467 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
11715433 TTATCGCCAC
11715443 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
11715468 TTGAAATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:11724503 original size:79 final size:79
Alignment explanation
Indices: 11724367--11724519 Score: 263
Period size: 79 Copynumber: 1.9 Consensus size: 79
11724357 AGTAGGAAAG
* *
11724367 TTAGCGTTTTCTCTTGACTTGGCCTTTATCTATACAATTTGACAGAGCAAGCTACATGTCTTCTT
1 TTAGCGTTTTCTCTTGACTTGGCCTTTATATATACAATTTGACAGAGCAAACTACATGTCTTCTT
11724432 AGGTAAGTTCACAT
66 AGGTAAGTTCACAT
*
11724446 TTAGTGTTTTCTCTTGACTTGGCCTTTATATATACTAA-TTGACAGAGCAAACTACATGTCTTCT
1 TTAGCGTTTTCTCTTGACTTGGCCTTTATATATAC-AATTTGACAGAGCAAACTACATGTCTTCT
11724510 TAGGTAAGTT
65 TAGGTAAGTT
11724520 AACGTTTCTG
Statistics
Matches: 70, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
79 68 0.97
80 2 0.03
ACGTcount: A:0.25, C:0.18, G:0.16, T:0.41
Consensus pattern (79 bp):
TTAGCGTTTTCTCTTGACTTGGCCTTTATATATACAATTTGACAGAGCAAACTACATGTCTTCTT
AGGTAAGTTCACAT
Found at i:11732402 original size:21 final size:19
Alignment explanation
Indices: 11732377--11732426 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 19
11732367 CATAAAATAG
*
11732377 ATTATTAATAAATATATATAT
1 ATTATTAATAAACATA-A-AT
11732398 ATTA-TATATAAACATAAAT
1 ATTATTA-ATAAACATAAAT
11732417 ATTATTAATA
1 ATTATTAATA
11732427 TTTTTAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
19 9 0.35
20 5 0.19
21 12 0.46
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (19 bp):
ATTATTAATAAACATAAAT
Found at i:11767447 original size:26 final size:24
Alignment explanation
Indices: 11767403--11767501 Score: 90
Period size: 27 Copynumber: 3.7 Consensus size: 24
11767393 TTCTTAAATA
11767403 TATTTTTAATATCATATATTTTATTTT
1 TATTTTT-ATAT-A-ATATTTTATTTT
11767430 TATTTATTAGTATAATATTTTATTTTT
1 TATTT-TTA-TATAATATTTTA-TTTT
11767457 TATTTTTAATATATTTATATTTTATTATT
1 TATTTTT-ATATA---ATATTTTATT-TT
*
11767486 AATTTTTATATAATAT
1 TATTTTTATATAATAT
11767502 CATTTCTTAA
Statistics
Matches: 63, Mismatches: 1, Indels: 18
0.77 0.01 0.22
Matches are distributed among these distances:
25 4 0.06
26 14 0.22
27 17 0.27
28 12 0.19
29 16 0.25
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.66
Consensus pattern (24 bp):
TATTTTTATATAATATTTTATTTT
Found at i:11767447 original size:28 final size:27
Alignment explanation
Indices: 11767350--11767605 Score: 112
Period size: 29 Copynumber: 9.0 Consensus size: 27
11767340 AATATAAGTC
* *
11767350 TAATATATTTATATTTTTATTATTAATTTT
1 TAATATA-ATATA-TTTTATT-TTTATTTT
** *
11767380 T-ATATAATATCATTTCTTAAATATATTTT
1 TAATATAATAT-A-TT-TTATTTTTATTTT
*
11767409 TAATATCATATATTTTATTTTTATTTAT
1 TAATATAATATATTTTATTTTTATTT-T
*
11767437 TAGTAT-A-ATATTTTATTTTTTATTTT
1 TAATATAATATATTTTA-TTTTTATTTT
* *
11767463 TAATATATTTATATTTTATTATTAATTTT
1 TAATATA-ATATATTTTATT-TTTATTTT
** *
11767492 T-ATATAATATCATTTCTTAAATATATTTT
1 TAATATAATAT-A-TT-TTATTTTTATTTT
* * *
11767521 TAATGTCATATATTTTTTTTATTTATTATT
1 TAATATAATATA-TTTTATT-TTTATT-TT
* * * *
11767551 ATATTTTTATATATTTTATTTTCATTTCTT
1 -TAATATAATATATTTTATTTTTA-TT-TT
11767581 TAATAT-AT-T-TTTTATATTTTATTTT
1 TAATATAATATATTTTAT-TTTTATTTT
11767606 ATTTTAATTT
Statistics
Matches: 175, Mismatches: 33, Indels: 41
0.70 0.13 0.16
Matches are distributed among these distances:
25 2 0.01
26 22 0.13
27 27 0.15
28 23 0.13
29 58 0.33
30 34 0.19
31 9 0.05
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.65
Consensus pattern (27 bp):
TAATATAATATATTTTATTTTTATTTT
Found at i:11767479 original size:22 final size:21
Alignment explanation
Indices: 11767424--11767496 Score: 80
Period size: 22 Copynumber: 3.5 Consensus size: 21
11767414 TCATATATTT
11767424 TATTTT-TA-TTTATTAGTATAA
1 TATTTTATATTTTATTA-T-TAA
* *
11767445 TATTTTATTTTTTATTTTTAA
1 TATTTTATATTTTATTATTAA
11767466 TATATTTATATTTTATTATTAA
1 TAT-TTTATATTTTATTATTAA
11767488 T-TTTTATAT
1 TATTTTATAT
11767497 AATATCATTT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
20 7 0.16
21 13 0.29
22 19 0.42
23 6 0.13
ACGTcount: A:0.30, C:0.00, G:0.01, T:0.68
Consensus pattern (21 bp):
TATTTTATATTTTATTATTAA
Found at i:11767554 original size:58 final size:58
Alignment explanation
Indices: 11767359--11767554 Score: 233
Period size: 58 Copynumber: 3.4 Consensus size: 58
11767349 CTAATATATT
*
11767359 TATATTTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAATATCA
1 TATATTTTTATTATTAATTATTATATAATATCATTTCTTAAATATATTTTTAATATCA
* * * * *
11767417 TATA-TTTTATTTTTATTTATTAGTATAATAT--TTTATT--TTTTATTTTTAATAT-A
1 TATATTTTTATTATTAATTATTA-TATAATATCATTTCTTAAATATATTTTTAATATCA
* * *
11767470 TTTATATTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAATGTCA
1 TATAT-TTTTATTATTAATTATTATATAATATCATTTCTTAAATATATTTTTAATATCA
* *
11767529 TATATTTTTTTTATTTATTATTATAT
1 TATATTTTTATTATTAATTATTATAT
11767555 TTTTATATAT
Statistics
Matches: 112, Mismatches: 18, Indels: 16
0.77 0.12 0.11
Matches are distributed among these distances:
53 4 0.04
54 21 0.19
55 15 0.13
56 10 0.09
57 15 0.13
58 42 0.38
59 5 0.04
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.63
Consensus pattern (58 bp):
TATATTTTTATTATTAATTATTATATAATATCATTTCTTAAATATATTTTTAATATCA
Found at i:11767566 original size:112 final size:113
Alignment explanation
Indices: 11767350--11767572 Score: 375
Period size: 112 Copynumber: 2.0 Consensus size: 113
11767340 AATATAAGTC
11767350 TAATATATTTATATTTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAATAT
1 TAATATATTTATATTTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAATAT
11767415 CATATATTTTATTTTTATTTATTAGTATAATATTTTATTTTTTATTTT
66 CATATATTTTATTTTTATTTATTAGTATAATATTTTATTTTTTATTTT
*
11767463 TAATATATTTATA-TTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAATGT
1 TAATATATTTATATTTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAATAT
*
11767527 CATATA-TTT-TTTTTATTTATTATTAT-AT-TTTTATATATTTTATTTT
66 CATATATTTTATTTTTATTTATTAGTATAATATTTTAT-T-TTTTATTTT
11767573 CATTTCTTTA
Statistics
Matches: 106, Mismatches: 2, Indels: 7
0.92 0.02 0.06
Matches are distributed among these distances:
108 6 0.06
109 3 0.03
110 25 0.24
111 3 0.03
112 56 0.53
113 13 0.12
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (113 bp):
TAATATATTTATATTTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAATAT
CATATATTTTATTTTTATTTATTAGTATAATATTTTATTTTTTATTTT
Found at i:11767586 original size:71 final size:70
Alignment explanation
Indices: 11767501--11767642 Score: 173
Period size: 71 Copynumber: 2.0 Consensus size: 70
11767491 TTATATAATA
* *
11767501 TCATTTCTTAAATATATTTTTAATGTCATATATTTT-TTTT-ATTTATTATTA-TATTTTTATAT
1 TCATTTCTTAAATATATTTTTAATAT--TATATTTTATTTTAATTT-TTATTATTA-TATTATAT
11767563 ATTTTATTT
62 ATTTTATTT
* * * *
11767572 TCATTTCTTTAATATATTTTTTATATTTTATTTTATTTTAATTTTTATTCTTATATTATATATTT
1 TCATTTCTTAAATATATTTTTAATATTATATTTTATTTTAATTTTTATTATTATATTATATATTT
11767637 TATTT
66 TATTT
11767642 T
1 T
11767643 AATATTTTTT
Statistics
Matches: 62, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
69 7 0.11
70 26 0.42
71 29 0.47
ACGTcount: A:0.27, C:0.04, G:0.01, T:0.68
Consensus pattern (70 bp):
TCATTTCTTAAATATATTTTTAATATTATATTTTATTTTAATTTTTATTATTATATTATATATTT
TATTT
Found at i:11767601 original size:33 final size:32
Alignment explanation
Indices: 11767528--11767609 Score: 114
Period size: 33 Copynumber: 2.6 Consensus size: 32
11767518 TTTTAATGTC
*
11767528 ATATATTTT-TTTTATTTATTATTATATTTTT
1 ATATATTTTATTTTATTTATTAATATATTTTT
*
11767559 ATATATTTTATTTTCATTTCTTTAATATATTTTT
1 ATATATTTTATTTT-ATTT-ATTAATATATTTTT
11767593 -TATATTTTATTTTATTT
1 ATATATTTTATTTTATTT
11767610 TAATTTTTAT
Statistics
Matches: 46, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
31 9 0.20
32 8 0.17
33 17 0.37
34 12 0.26
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (32 bp):
ATATATTTTATTTTATTTATTAATATATTTTT
Found at i:11767602 original size:7 final size:7
Alignment explanation
Indices: 11767590--11767658 Score: 54
Period size: 7 Copynumber: 9.7 Consensus size: 7
11767580 TTAATATATT
11767590 TTTTATA
1 TTTTATA
11767597 TTTTATTTTA
1 TTTTA---TA
11767607 TTTTA-A
1 TTTTATA
11767613 TTTT-TA
1 TTTTATA
11767619 TTCTTATA
1 TT-TTATA
*
11767627 TTATATA
1 TTTTATA
11767634 TTTTAT-
1 TTTTATA
*
11767640 TTTAATA
1 TTTTATA
*
11767647 TTTTTTA
1 TTTTATA
11767654 TTTTA
1 TTTTA
11767659 ATTATAATAT
Statistics
Matches: 49, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
6 13 0.27
7 25 0.51
8 4 0.08
10 7 0.14
ACGTcount: A:0.26, C:0.01, G:0.00, T:0.72
Consensus pattern (7 bp):
TTTTATA
Found at i:11767608 original size:38 final size:37
Alignment explanation
Indices: 11767501--11767615 Score: 98
Period size: 38 Copynumber: 3.2 Consensus size: 37
11767491 TTATATAATA
* * *
11767501 TCATTTCTTAAATATATTTTTAATGTCATATATTTT-TTT
1 TCATTTCTTTAATATATTTTT--TAT-ATTTATTTTATTT
* *
11767540 T-ATTT-ATTATTATA-TTTTTATA--TATTTTATTT
1 TCATTTCTTTAATATATTTTTTATATTTATTTTATTT
11767572 TCATTTCTTTAATATATTTTTTATATTTTATTTTATTT
1 TCATTTCTTTAATATATTTTTTATA-TTTATTTTATTT
*
11767610 TAATTT
1 TCATTT
11767616 TTATTCTTAT
Statistics
Matches: 62, Mismatches: 7, Indels: 15
0.74 0.08 0.18
Matches are distributed among these distances:
31 6 0.10
32 4 0.06
33 5 0.08
34 9 0.15
35 8 0.13
36 4 0.06
37 6 0.10
38 19 0.31
39 1 0.02
ACGTcount: A:0.27, C:0.04, G:0.01, T:0.68
Consensus pattern (37 bp):
TCATTTCTTTAATATATTTTTTATATTTATTTTATTT
Found at i:11767610 original size:43 final size:43
Alignment explanation
Indices: 11767544--11767657 Score: 110
Period size: 43 Copynumber: 2.7 Consensus size: 43
11767534 TTTTTTTATT
*
11767544 TATTATTATATTTT-TATATATTTTATTTTCATTTCTT-TAATATA
1 TATT-TTATATTTTAT-TTTATTTTATTTTCA-TTCTTATAATATA
* * *
11767588 TTTTTTATATTTTATTTTATTTTAATTTTTATTCTTATATTATA
1 TATTTTATATTTTATTTTATTTT-ATTTTCATTCTTATAATATA
* *
11767632 TATTTTAT-TTTAATATT-TTTTATTTT
1 TATTTTATATTTTATTTTATTTTATTTT
11767658 AATTATAATA
Statistics
Matches: 60, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
41 5 0.08
42 4 0.07
43 28 0.47
44 23 0.38
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (43 bp):
TATTTTATATTTTATTTTATTTTATTTTCATTCTTATAATATA
Found at i:11767625 original size:6 final size:5
Alignment explanation
Indices: 11767531--11767658 Score: 56
Period size: 5 Copynumber: 25.4 Consensus size: 5
11767521 TAATGTCATA
11767531 TATTT T-TTT TA-TT TATTAT TATATT T-TTAT ATATTT TATTT TCA-TT
1 TATTT TATTT TATTT TATT-T TAT-TT TATT-T -TATTT TATTT T-ATTT
* * * *
11767577 T-CTT TAATA TATTT T-TTA TATTT TATTT TATTT TAATTTT TATTCT
1 TATTT TATTT TATTT TATTT TATTT TATTT TATTT T-A-TTT TATT-T
* * *
11767623 TATAT TA-TA TATTT TATTT TAATAT T-TTT TATTT TA
1 TATTT TATTT TATTT TATTT T-ATTT TATTT TATTT TA
11767659 ATTATAATAT
Statistics
Matches: 94, Mismatches: 12, Indels: 34
0.67 0.09 0.24
Matches are distributed among these distances:
4 20 0.21
5 48 0.51
6 19 0.20
7 7 0.07
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (5 bp):
TATTT
Found at i:11779121 original size:23 final size:23
Alignment explanation
Indices: 11779077--11779119 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
11779067 TTAAAATTGG
*
11779077 AATTTTTAATAATAGAAAAAATA
1 AATTTATAATAATAGAAAAAATA
11779100 AATTTATAAT-ATAGAAAAAA
1 AATTTATAATAATAGAAAAAA
11779120 ATTAAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.33
Consensus pattern (23 bp):
AATTTATAATAATAGAAAAAATA
Found at i:11782575 original size:2 final size:2
Alignment explanation
Indices: 11782568--11782597 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
11782558 AAAGAGCTGA
11782568 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
11782598 GATGAAGAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:11788395 original size:6 final size:6
Alignment explanation
Indices: 11788384--11788408 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
11788374 AAGCCCCCAG
11788384 CGCACC CGCACC CGCACC CGCACC C
1 CGCACC CGCACC CGCACC CGCACC C
11788409 ACGCGCACCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.68, G:0.16, T:0.00
Consensus pattern (6 bp):
CGCACC
Found at i:11809056 original size:2 final size:2
Alignment explanation
Indices: 11809049--11809078 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
11809039 TCTATTTTTC
11809049 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
11809079 GCTAAGGACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:11864359 original size:2 final size:2
Alignment explanation
Indices: 11864352--11864381 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
11864342 CTCTTATCCC
11864352 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
11864382 ATGGTACTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:11870563 original size:5 final size:5
Alignment explanation
Indices: 11870553--11870577 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
11870543 TTTATTGACC
11870553 CCCTG CCCTG CCCTG CCCTG CCCTG
1 CCCTG CCCTG CCCTG CCCTG CCCTG
11870578 ACAAGAATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.60, G:0.20, T:0.20
Consensus pattern (5 bp):
CCCTG
Found at i:11889148 original size:27 final size:27
Alignment explanation
Indices: 11889118--11889188 Score: 133
Period size: 27 Copynumber: 2.6 Consensus size: 27
11889108 CTCCTCGTCG
11889118 TCGTCTTCTTCATCTTCATCTTCATCT
1 TCGTCTTCTTCATCTTCATCTTCATCT
11889145 TCGTCTTCTTCATCTTCATCTTCATCT
1 TCGTCTTCTTCATCTTCATCTTCATCT
*
11889172 TCGTCGTCTTCATCTTC
1 TCGTCTTCTTCATCTTC
11889189 TTCAGCTTCA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.10, C:0.34, G:0.06, T:0.51
Consensus pattern (27 bp):
TCGTCTTCTTCATCTTCATCTTCATCT
Found at i:11889154 original size:21 final size:21
Alignment explanation
Indices: 11889121--11889198 Score: 93
Period size: 21 Copynumber: 3.7 Consensus size: 21
11889111 CTCGTCGTCG
11889121 TCTTCTTCATCTTCATCTTCA
1 TCTTCTTCATCTTCATCTTCA
* *
11889142 TCTTCGTCTTCTTCATCTTCA
1 TCTTCTTCATCTTCATCTTCA
* * * *
11889163 TCTTCATCTTCGTCGTCTTCA
1 TCTTCTTCATCTTCATCTTCA
*
11889184 TCTTCTTCAGCTTCA
1 TCTTCTTCATCTTCA
11889199 GGCTCACTCT
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.12, C:0.33, G:0.05, T:0.50
Consensus pattern (21 bp):
TCTTCTTCATCTTCATCTTCA
Found at i:11889188 original size:6 final size:6
Alignment explanation
Indices: 11889124--11889173 Score: 70
Period size: 6 Copynumber: 8.8 Consensus size: 6
11889114 GTCGTCGTCT
*
11889124 TCTTCA TCTTCA TCTTCA TCTTCG TC-T-- TCTTCA TCTTCA TCTTCA
1 TCTTCA TCTTCA TCTTCA TCTTCA TCTTCA TCTTCA TCTTCA TCTTCA
11889169 TCTTC
1 TCTTC
11889174 GTCGTCTTCA
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
3 2 0.05
4 1 0.03
5 1 0.03
6 36 0.90
ACGTcount: A:0.12, C:0.34, G:0.02, T:0.52
Consensus pattern (6 bp):
TCTTCA
Found at i:11889482 original size:6 final size:6
Alignment explanation
Indices: 11889473--11889498 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
11889463 GCCGAAGCCG
11889473 AACCCA AACCCA AACCCA AACCCA AA
1 AACCCA AACCCA AACCCA AACCCA AA
11889499 ACTATGGCGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.54, C:0.46, G:0.00, T:0.00
Consensus pattern (6 bp):
AACCCA
Found at i:11895860 original size:5 final size:5
Alignment explanation
Indices: 11895850--11895883 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
11895840 GAATAAATCT
11895850 GGATG GGATG GGATG GGATG GGATG GGATG GGAT
1 GGATG GGATG GGATG GGATG GGATG GGATG GGAT
11895884 ATATTATAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.21, C:0.00, G:0.59, T:0.21
Consensus pattern (5 bp):
GGATG
Found at i:11911607 original size:20 final size:21
Alignment explanation
Indices: 11911569--11911608 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
11911559 AGTATTAGAA
* *
11911569 AGAGAAATATGAAATCATAAG
1 AGAGAAATACGAAAACATAAG
11911590 AGAGAAAT-CGAAAACATAA
1 AGAGAAATACGAAAACATAA
11911609 TAGACAAACG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.60, C:0.07, G:0.17, T:0.15
Consensus pattern (21 bp):
AGAGAAATACGAAAACATAAG
Found at i:11918355 original size:25 final size:26
Alignment explanation
Indices: 11918327--11918390 Score: 80
Period size: 25 Copynumber: 2.5 Consensus size: 26
11918317 AAAGTATATC
11918327 ATATTAATTAT-ATATAA-AATAATTA
1 ATATTAATTATAAT-TAATAATAATTA
*
11918352 ATATT-ATTTTAATTAATAATAATTA
1 ATATTAATTATAATTAATAATAATTA
11918377 ATTATTAATTATAA
1 A-TATTAATTATAA
11918391 AAATATATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
24 7 0.21
25 16 0.48
26 4 0.12
27 6 0.18
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (26 bp):
ATATTAATTATAATTAATAATAATTA
Found at i:11923357 original size:17 final size:17
Alignment explanation
Indices: 11923330--11923364 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
11923320 TAATAATTTA
11923330 ATTTAAATTAAA-AATT
1 ATTTAAATTAAATAATT
11923346 ATTTACAATTAAATAATT
1 ATTTA-AATTAAATAATT
11923364 A
1 A
11923365 AAACTTAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.29
17 7 0.41
18 5 0.29
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (17 bp):
ATTTAAATTAAATAATT
Found at i:11929917 original size:19 final size:19
Alignment explanation
Indices: 11929880--11929918 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
11929870 TAGTTAGAAA
* *
11929880 CTAGTCGCAAGCGGTGACG
1 CTAGTCGCAAGCAGAGACG
*
11929899 CTAGTTGCAAGCAGAGACG
1 CTAGTCGCAAGCAGAGACG
11929918 C
1 C
11929919 AACTTAAAAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.26, C:0.26, G:0.33, T:0.15
Consensus pattern (19 bp):
CTAGTCGCAAGCAGAGACG
Found at i:11931982 original size:2 final size:2
Alignment explanation
Indices: 11931975--11932010 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
11931965 AAATCTTTAA
* *
11931975 AT AT AT AT AT AT AT AT AT AT AT GT AT GT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11932011 TCATTTCAGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11934694 original size:2 final size:2
Alignment explanation
Indices: 11934683--11934719 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
11934673 TTTTTGTTAT
11934683 TA TA TA -A 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
11934720 AAGAAGAAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:11949320 original size:6 final size:6
Alignment explanation
Indices: 11949309--11949341 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
11949299 TCTATCTGCT
11949309 CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTC
1 CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTC
11949342 ATGGGTAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.00, C:0.67, G:0.00, T:0.33
Consensus pattern (6 bp):
CTCTCC
Found at i:11949910 original size:2 final size:2
Alignment explanation
Indices: 11949905--11949947 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
11949895 AATGTGTGTG
11949905 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
11949947 T
1 T
11949948 CTACATTATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:11951989 original size:2 final size:2
Alignment explanation
Indices: 11951982--11952024 Score: 61
Period size: 2 Copynumber: 21.5 Consensus size: 2
11951972 CTACACATAC
*
11951982 AT AT AT AT AT AT AT AT AT AT AT AT -T CAC 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
11952024 A
1 A
11952025 ATGGTAATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:11972470 original size:21 final size:21
Alignment explanation
Indices: 11972444--11972483 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
11972434 AATATAAAAA
11972444 TATTATGTTATT-TTTTAATAT
1 TATTAT-TTATTATTTTAATAT
11972465 TATTATTTATTATTTTAAT
1 TATTATTTATTATTTTAAT
11972484 TAATTAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (21 bp):
TATTATTTATTATTTTAATAT
Found at i:11973730 original size:2 final size:2
Alignment explanation
Indices: 11973717--11973746 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
11973707 TCAGTCCTAG
*
11973717 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11973747 GCTTCCACAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:11976747 original size:13 final size:13
Alignment explanation
Indices: 11976729--11976753 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11976719 CACACCTACC
11976729 CTATATATATATA
1 CTATATATATATA
11976742 CTATATATATAT
1 CTATATATATAT
11976754 GTAGAGAGTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (13 bp):
CTATATATATATA
Found at i:11980232 original size:4 final size:4
Alignment explanation
Indices: 11980223--11980249 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
11980213 TCCTCATCAT
11980223 ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATA
11980250 ATTTGTTGGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.22, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:11989455 original size:22 final size:22
Alignment explanation
Indices: 11989429--11989474 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
11989419 GGTAGAGAAA
11989429 GAACTATAAAGCATCAGAAATG
1 GAACTATAAAGCATCAGAAATG
11989451 GAACTATAAAGCATCAGAAATG
1 GAACTATAAAGCATCAGAAATG
11989473 GA
1 GA
11989475 TGGCACCTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.50, C:0.13, G:0.20, T:0.17
Consensus pattern (22 bp):
GAACTATAAAGCATCAGAAATG
Found at i:12002152 original size:2 final size:2
Alignment explanation
Indices: 12002145--12002190 Score: 74
Period size: 2 Copynumber: 22.5 Consensus size: 2
12002135 CATTCCTCAA
*
12002145 AT AT AT AT AT ACT AT TT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12002188 AT A
1 AT A
12002191 GCCTACCTCT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
2 39 0.95
3 2 0.05
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12009672 original size:2 final size:2
Alignment explanation
Indices: 12009667--12009699 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
12009657 TGTGTGTGTT
*
12009667 TA TA TA TT 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
12009700 GCGCCATAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:12015988 original size:2 final size:2
Alignment explanation
Indices: 12015981--12016010 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
12015971 TTTGGATGGA
*
12015981 AT AT AT AT AT AC 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
12016011 CGCCAAACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:12016713 original size:43 final size:43
Alignment explanation
Indices: 12016652--12016739 Score: 149
Period size: 43 Copynumber: 2.0 Consensus size: 43
12016642 CATCACGAGC
*
12016652 AGCACTGATCATGTCAAGGCAACAGGGATAGTAAACACAGCTT
1 AGCACTAATCATGTCAAGGCAACAGGGATAGTAAACACAGCTT
* *
12016695 AGCACTAATCATGTCAAGGCAACGGGGATAGTAAATACAGCTT
1 AGCACTAATCATGTCAAGGCAACAGGGATAGTAAACACAGCTT
12016738 AG
1 AG
12016740 ATAAGAGATC
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.38, C:0.19, G:0.24, T:0.19
Consensus pattern (43 bp):
AGCACTAATCATGTCAAGGCAACAGGGATAGTAAACACAGCTT
Found at i:12017110 original size:43 final size:43
Alignment explanation
Indices: 12017046--12017135 Score: 162
Period size: 43 Copynumber: 2.1 Consensus size: 43
12017036 CAAATCGCAC
12017046 TACGGATTCTACTTCTATACACCCAGACCAAAGAAACATTTCA
1 TACGGATTCTACTTCTATACACCCAGACCAAAGAAACATTTCA
* *
12017089 TACGGATTCTATTTCTTTACACCCAGACCAAAGAAACATTTCA
1 TACGGATTCTACTTCTATACACCCAGACCAAAGAAACATTTCA
12017132 TACG
1 TACG
12017136 TTATACACCT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.36, C:0.27, G:0.10, T:0.28
Consensus pattern (43 bp):
TACGGATTCTACTTCTATACACCCAGACCAAAGAAACATTTCA
Found at i:12019675 original size:2 final size:2
Alignment explanation
Indices: 12019668--12019697 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
12019658 TTAAGAAACA
12019668 AG AG AG AG AG AG AG -G AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
12019698 ATATGTCCTG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:12019687 original size:13 final size:13
Alignment explanation
Indices: 12019669--12019694 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12019659 TAAGAAACAA
12019669 GAGAGAGAGAGAG
1 GAGAGAGAGAGAG
12019682 GAGAGAGAGAGAG
1 GAGAGAGAGAGAG
12019695 AGAATATGTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.54, T:0.00
Consensus pattern (13 bp):
GAGAGAGAGAGAG
Found at i:12019688 original size:15 final size:15
Alignment explanation
Indices: 12019668--12019696 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
12019658 TTAAGAAACA
12019668 AGAGAGAGAGAGAGG
1 AGAGAGAGAGAGAGG
12019683 AGAGAGAGAGAGAG
1 AGAGAGAGAGAGAG
12019697 AATATGTCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (15 bp):
AGAGAGAGAGAGAGG
Found at i:12020389 original size:12 final size:13
Alignment explanation
Indices: 12020372--12020400 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
12020362 TACATATTAT
12020372 ATAAATTTT-TTA
1 ATAAATTTTCTTA
12020384 ATAAATTTTCTTA
1 ATAAATTTTCTTA
12020397 ATAA
1 ATAA
12020401 CCTCCCAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (13 bp):
ATAAATTTTCTTA
Found at i:12020508 original size:12 final size:11
Alignment explanation
Indices: 12020493--12020544 Score: 54
Period size: 12 Copynumber: 4.6 Consensus size: 11
12020483 TAATATTATT
12020493 TTTATTTTTTAA
1 TTTATTTTTT-A
12020505 TTTATTTTGTTA
1 TTTATTTT-TTA
*
12020517 TTTA-TATTTA
1 TTTATTTTTTA
12020527 TTTA-TTTTTA
1 TTTATTTTTTA
12020537 TTCTATTT
1 TT-TATTT
12020545 ACTCATATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
10 14 0.40
11 4 0.11
12 15 0.43
13 2 0.06
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.75
Consensus pattern (11 bp):
TTTATTTTTTA
Found at i:12020509 original size:18 final size:18
Alignment explanation
Indices: 12020480--12020538 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 18
12020470 GGTGACTCAA
12020480 TTTTAATATTATTTTTATT
1 TTTTAAT-TTATTTTTATT
12020499 TTTTAATTTATTTTGTTATT
1 TTTTAATTTA-TTT-TTATT
*
12020519 TATATTTATTTATTTTTATT
1 T-T-TTAATTTATTTTTATT
12020539 CTATTTACTC
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
18 3 0.09
19 10 0.29
20 11 0.31
21 4 0.11
22 7 0.20
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.75
Consensus pattern (18 bp):
TTTTAATTTATTTTTATT
Found at i:12020512 original size:17 final size:17
Alignment explanation
Indices: 12020480--12020535 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
12020470 GGTGACTCAA
12020480 TTTTAATATTATTTTTATT
1 TTTTAAT-TTA-TTTTATT
*
12020499 TTTTAATTTATTTTGTT
1 TTTTAATTTATTTTATT
*
12020516 ATTTATATTTA-TTTATT
1 TTTTA-ATTTATTTTATT
12020533 TTT
1 TTT
12020536 ATTCTATTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
17 17 0.53
18 8 0.25
19 7 0.22
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (17 bp):
TTTTAATTTATTTTATT
Found at i:12022269 original size:22 final size:23
Alignment explanation
Indices: 12022212--12022272 Score: 61
Period size: 26 Copynumber: 2.6 Consensus size: 23
12022202 NNNNTATTTG
* *
12022212 GCATTACGTGACTGAATATTTGTTGA
1 GCATTACGTGACT---TGTTTGTAGA
*
12022238 GCATTGCGTGACTTGTTTGTAGA
1 GCATTACGTGACTTGTTTGTAGA
12022261 -CATTACGTGACT
1 GCATTACGTGACT
12022273 AAATGTTATA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
22 11 0.35
23 8 0.26
26 12 0.39
ACGTcount: A:0.23, C:0.15, G:0.25, T:0.38
Consensus pattern (23 bp):
GCATTACGTGACTTGTTTGTAGA
Found at i:12024398 original size:170 final size:170
Alignment explanation
Indices: 12024116--12024439 Score: 470
Period size: 170 Copynumber: 1.9 Consensus size: 170
12024106 ACGTGATTGG
* * * * *
12024116 TTATGTTGGCATAACGTGAGTGGATATTAGACATCGAGTGACTTATTATTAGGTATTGCGAGACT
1 TTATGTTAGCATAACGTGAGTAGATATTAGACATCAAGTGACTTATTAATAAGTATTGCGAGACT
* *
12024181 AGAGGTGCATGACTTGTGCAATTCATCTCTTGTTTTAAGGCTTTTGTTCAGTAGTTTGTAGGCAT
66 AGAGGTGCATGACTTGTGCAATTCATCTCTTGTTTTAAGGATTTTGTTCAGTAGTTTGTAGGCAC
* *
12024246 TGTGTGATTGATTTTTATATATTGTGTAATATTGAGTTGT
131 TATGTGACTGATTTTTATATATTGTGTAATATTGAGTTGT
* * *
12024286 TTATGTTAGCATAATGTGAGTAGATATTACG-CATTAAGTGACTTATTAATAAGTATTGCGAGAT
1 TTATGTTAGCATAACGTGAGTAGATATTA-GACATCAAGTGACTTATTAATAAGTATTGCGAGAC
* * * * *
12024350 TAGAGGTGCGTGACTTGTGCAATTCATCTTTTGTTTTGAGGATTTTGTTTAGTAGTTTGTAGGTA
65 TAGAGGTGCATGACTTGTGCAATTCATCTCTTGTTTTAAGGATTTTGTTCAGTAGTTTGTAGGCA
*
12024415 CTATGTGACTGATTTTTATTTATTG
130 CTATGTGACTGATTTTTATATATTG
12024440 CATCACTTGT
Statistics
Matches: 135, Mismatches: 18, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
170 134 0.99
171 1 0.01
ACGTcount: A:0.24, C:0.09, G:0.24, T:0.43
Consensus pattern (170 bp):
TTATGTTAGCATAACGTGAGTAGATATTAGACATCAAGTGACTTATTAATAAGTATTGCGAGACT
AGAGGTGCATGACTTGTGCAATTCATCTCTTGTTTTAAGGATTTTGTTCAGTAGTTTGTAGGCAC
TATGTGACTGATTTTTATATATTGTGTAATATTGAGTTGT
Found at i:12024635 original size:203 final size:201
Alignment explanation
Indices: 12024286--12024820 Score: 712
Period size: 203 Copynumber: 2.6 Consensus size: 201
12024276 ATTGAGTTGT
* * * * *
12024286 TTATGTTAGCATAATGTGAGTAGATATTACGCATTAAGTGACTTATTAATAAGTATTGCGAGATT
1 TTATGTTGGCATAATGTGAGTGGATATTATGCATTGAGTGACTTATTATTAAGTATTGCGAGA--
* * * * *
12024351 AGAGGTGCGTGACTTGTGCAATTCATCTTTTGTTTTGAGGATTTTGTTTAGTAGTTTGTAGGTAC
64 AGAGGTGTGTGACTTGTGCAATTCATCTTTTGTTTTGAGGCTTTTGTTCACTAGTTTGTAGGCAC
* * * * *
12024416 TATGTGACTGATTTTTATTTATTG-CATCACTTGTTGTTATGTATTGCGTGACATTGAGCCGTTA
129 TACGTGACTGATTTTTATGTA-TGACATCACCTATTATTATGTATTGCGTGACATTGAGCCGTTA
12024480 CATGACTGG
193 CATGACTGG
* * *
12024489 TTATGTTGGCATAATATGAGTGGATACTATGCATTGACTGACTTATTATTAAGTATTGCGAGACA
1 TTATGTTGGCATAATGTGAGTGGATATTATGCATTGAGTGACTTATTATTAAGTATTGCGAGA-A
*
12024554 GGAGGTGTGTGACTTGTGCAATTCATCTTTTGTTTTGAAGCTTTTGTTCACTAGTTTGTAGGCAC
65 -GAGGTGTGTGACTTGTGCAATTCATCTTTTGTTTTGAGGCTTTTGTTCACTAGTTTGTAGGCAC
* * * * * *
12024619 TGCGTGACTGATTTTTATGTATGACATGACCTATTATTATGTGTTGCGTGACATTGGGGCTTTAC
129 TACGTGACTGATTTTTATGTATGACATCACCTATTATTATGTATTGCGTGACATTGAGCCGTTAC
*
12024684 GTGACTGG
194 ATGACTGG
* *
12024692 TTATGTTGGCATAATGTGAGTGGATATTATGCATTGAGTGACTTATTATTAGGTATTGCGAGATT
1 TTATGTTGGCATAATGTGAGTGGATATTATGCATTGAGTGACTTATTATTAAGTATTGCGAGA-A
* * * *
12024757 GACGGTGTGTGACTTGTACAATTCATCTCTTGTTTTGAGGCTTTTGTTCGCTAGTTTTTAGGCA
65 GA-GGTGTGTGACTTGTGCAATTCATCTTTTGTTTTGAGGCTTTTGTTCACTAGTTTGTAGGCA
12024821 TTGCATGAAT
Statistics
Matches: 291, Mismatches: 38, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
202 5 0.02
203 286 0.98
ACGTcount: A:0.23, C:0.11, G:0.24, T:0.41
Consensus pattern (201 bp):
TTATGTTGGCATAATGTGAGTGGATATTATGCATTGAGTGACTTATTATTAAGTATTGCGAGAAG
AGGTGTGTGACTTGTGCAATTCATCTTTTGTTTTGAGGCTTTTGTTCACTAGTTTGTAGGCACTA
CGTGACTGATTTTTATGTATGACATCACCTATTATTATGTATTGCGTGACATTGAGCCGTTACAT
GACTGG
Found at i:12025305 original size:42 final size:42
Alignment explanation
Indices: 12025199--12025297 Score: 144
Period size: 42 Copynumber: 2.4 Consensus size: 42
12025189 AGTACAAGAT
* * * *
12025199 ATGCCATAACTGTTGTGTTTGAAGAAGTTCAGTTTGATGACC
1 ATGCCACAACTGTTGTGTTAGAAGAAGTTCAGTTCGACGACC
* *
12025241 ATGCCACAACTGTTGTGTTAGAAGAGGTTTAGTTCGACGACC
1 ATGCCACAACTGTTGTGTTAGAAGAAGTTCAGTTCGACGACC
12025283 ATGCCACAACTGTTG
1 ATGCCACAACTGTTG
12025298 AATTAGAAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.31
Consensus pattern (42 bp):
ATGCCACAACTGTTGTGTTAGAAGAAGTTCAGTTCGACGACC
Found at i:12031657 original size:23 final size:23
Alignment explanation
Indices: 12031631--12031723 Score: 64
Period size: 23 Copynumber: 4.0 Consensus size: 23
12031621 TGGTAACGTC
12031631 ACTCCATATATACTACTCACGCA
1 ACTCCATATATACTACTCACGCA
* * * * *
12031654 ACTCAATATCA-ATTAATCATGCG
1 ACTCCATAT-ATACTACTCACGCA
* * *
12031677 ATTCCATA-ATAACTAGTCACGCG
1 ACTCCATATAT-ACTACTCACGCA
* *
12031700 ACTTCATATTTACTACTCACGCA
1 ACTCCATATATACTACTCACGCA
12031723 A
1 A
12031724 TTTTATAACA
Statistics
Matches: 51, Mismatches: 15, Indels: 8
0.69 0.20 0.11
Matches are distributed among these distances:
21 1 0.02
23 48 0.94
24 2 0.04
ACGTcount: A:0.35, C:0.28, G:0.08, T:0.29
Consensus pattern (23 bp):
ACTCCATATATACTACTCACGCA
Found at i:12031832 original size:23 final size:23
Alignment explanation
Indices: 12031792--12031853 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
12031782 CTCATGCGAC
* *
12031792 TCCATATTTATTAATCACACGAT
1 TCCATATTTACTAGTCACACGAT
* **
12031815 TTCATATTTACTAGTCACGTGAT
1 TCCATATTTACTAGTCACACGAT
*
12031838 TCCATATTAACTAGTC
1 TCCATATTTACTAGTC
12031854 GTGTGATTCC
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.31, C:0.21, G:0.08, T:0.40
Consensus pattern (23 bp):
TCCATATTTACTAGTCACACGAT
Found at i:12031859 original size:23 final size:23
Alignment explanation
Indices: 12031812--12031909 Score: 97
Period size: 23 Copynumber: 4.3 Consensus size: 23
12031802 TTAATCACAC
* *
12031812 GATTTCATATTTACTAGTCACGT
1 GATTCCATATTAACTAGTCACGT
**
12031835 GATTCCATATTAACTAGTCGTGT
1 GATTCCATATTAACTAGTCACGT
* * *
12031858 GATTCCATATCAAATACTCACGT
1 GATTCCATATTAACTAGTCACGT
* * * *
12031881 GAATCAATATCAACTAGTGACGT
1 GATTCCATATTAACTAGTCACGT
12031904 GATTCC
1 GATTCC
12031910 GTATCAACCA
Statistics
Matches: 59, Mismatches: 16, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 59 1.00
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (23 bp):
GATTCCATATTAACTAGTCACGT
Found at i:12031914 original size:23 final size:23
Alignment explanation
Indices: 12031824--12031917 Score: 107
Period size: 23 Copynumber: 4.1 Consensus size: 23
12031814 TTTCATATTT
*
12031824 ACTAGTCACGTGATTCCATATTA
1 ACTAGTCACGTGATTCCATATCA
**
12031847 ACTAGTCGTGTGATTCCATATCA
1 ACTAGTCACGTGATTCCATATCA
* * * *
12031870 AATACTCACGTGAATCAATATCA
1 ACTAGTCACGTGATTCCATATCA
* *
12031893 ACTAGTGACGTGATTCCGTATCA
1 ACTAGTCACGTGATTCCATATCA
12031916 AC
1 AC
12031918 CATTCACGCA
Statistics
Matches: 56, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 56 1.00
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.31
Consensus pattern (23 bp):
ACTAGTCACGTGATTCCATATCA
Found at i:12031925 original size:46 final size:46
Alignment explanation
Indices: 12031829--12031939 Score: 109
Period size: 46 Copynumber: 2.4 Consensus size: 46
12031819 TATTTACTAG
* * * * *
12031829 TCACGTGATTCCATATTAACTAGTCGTGTGATTCCATATCAAATAC
1 TCACGTGAATCAATATCAACTAGTCGCGTGATTCCATATCAAACAC
* * *
12031875 TCACGTGAATCAATATCAACTAGT-GACGTGATTCCGTATCAACCAT
1 TCACGTGAATCAATATCAACTAGTCG-CGTGATTCCATATCAAACAC
*
12031921 TCACG-CAATTCAATATCAA
1 TCACGTGAA-TCAATATCAA
12031940 TTGATTACAA
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
45 3 0.06
46 51 0.94
ACGTcount: A:0.33, C:0.23, G:0.13, T:0.31
Consensus pattern (46 bp):
TCACGTGAATCAATATCAACTAGTCGCGTGATTCCATATCAAACAC
Found at i:12032205 original size:26 final size:26
Alignment explanation
Indices: 12032163--12032228 Score: 78
Period size: 26 Copynumber: 2.5 Consensus size: 26
12032153 TTTTTTGTGT
*
12032163 TAAATGATATAAAAAAGAAAAATATG
1 TAAATGATACAAAAAAGAAAAATATG
* *
12032189 TAAATGATACAACAAAGAATAATATG
1 TAAATGATACAAAAAAGAAAAATATG
* * *
12032215 GACATGAGACAAAA
1 TAAATGATACAAAA
12032229 CAATGTTATT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.61, C:0.06, G:0.14, T:0.20
Consensus pattern (26 bp):
TAAATGATACAAAAAAGAAAAATATG
Found at i:12034209 original size:12 final size:12
Alignment explanation
Indices: 12034192--12034231 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
12034182 CAGCATAAGG
12034192 AGCATCAGGAGA
1 AGCATCAGGAGA
* *
12034204 AGCATCATGAGG
1 AGCATCAGGAGA
12034216 AGCATCAGGAGA
1 AGCATCAGGAGA
12034228 AGCA
1 AGCA
12034232 GCATAAAGAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.40, C:0.17, G:0.33, T:0.10
Consensus pattern (12 bp):
AGCATCAGGAGA
Found at i:12034249 original size:24 final size:24
Alignment explanation
Indices: 12034173--12034242 Score: 95
Period size: 24 Copynumber: 2.9 Consensus size: 24
12034163 ATAATTATAG
* *
12034173 CAGGAGTATCAGCATAAGGAGCAT
1 CAGGAGAAGCAGCATAAGGAGCAT
* *
12034197 CAGGAGAAGCATCATGAGGAGCAT
1 CAGGAGAAGCAGCATAAGGAGCAT
*
12034221 CAGGAGAAGCAGCATAAAGAGC
1 CAGGAGAAGCAGCATAAGGAGC
12034243 CCCAGGAAGA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.40, C:0.17, G:0.31, T:0.11
Consensus pattern (24 bp):
CAGGAGAAGCAGCATAAGGAGCAT
Found at i:12036352 original size:23 final size:23
Alignment explanation
Indices: 12036300--12036355 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
12036290 CAGTCACGTT
* *
12036300 GTCACGCAATGATTTATCAATAG
1 GTCACGCAATAACTTATCAATAG
*
12036323 GTAACGCAATAACTTATCAATCA-
1 GTCACGCAATAACTTATCAAT-AG
12036346 GTCACGCAAT
1 GTCACGCAAT
12036356 GTTAATCCCT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 27 0.96
24 1 0.04
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.27
Consensus pattern (23 bp):
GTCACGCAATAACTTATCAATAG
Found at i:12037879 original size:21 final size:22
Alignment explanation
Indices: 12037839--12037882 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
12037829 GGTCATATCC
12037839 TTTTTTTAAAATCCAATTTTGG
1 TTTTTTTAAAATCCAATTTTGG
* *
12037861 TTTTTTTATAAT-CATTTTTGG
1 TTTTTTTAAAATCCAATTTTGG
12037882 T
1 T
12037883 ATACATGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.23, C:0.07, G:0.09, T:0.61
Consensus pattern (22 bp):
TTTTTTTAAAATCCAATTTTGG
Found at i:12042461 original size:110 final size:111
Alignment explanation
Indices: 12042299--12042512 Score: 315
Period size: 110 Copynumber: 1.9 Consensus size: 111
12042289 TATGGATTGA
*
12042299 TGCATGAAACAGGTTTTAAATGCCTAATTCTCATATATGTTATTACCAGGAAAGAACAGTACAT-
1 TGCATGAAACAAGTTTTAAATGCCTAATTCTCATATATGTTATTACCAGGAAAGAACAGTACATA
* * *
12042363 ACA-AATCTTATGAATTCTGTCCATGAAGATTATATTATAGACTGT
66 AAAGAATCTTACGAATTCTGTACATGAAGATTATATTATAGACTGT
* * *
12042408 TGCATGAAACAAGTTTTCAATGCCTTAATTCTCATATGTGTTGTTACCAGGAAAGAACAGTACAT
1 TGCATGAAACAAGTTTTAAATGCC-TAATTCTCATATATGTTATTACCAGGAAAGAACAGTACAT
* * *
12042473 AAAAGAATTTTGCGAATTGTGTACATGAAGATTATATTAT
65 AAAAGAATCTTACGAATTCTGTACATGAAGATTATATTAT
12042513 CACTGTTCAA
Statistics
Matches: 92, Mismatches: 10, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
109 22 0.24
110 38 0.41
111 2 0.02
112 30 0.33
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (111 bp):
TGCATGAAACAAGTTTTAAATGCCTAATTCTCATATATGTTATTACCAGGAAAGAACAGTACATA
AAAGAATCTTACGAATTCTGTACATGAAGATTATATTATAGACTGT
Found at i:12054509 original size:29 final size:31
Alignment explanation
Indices: 12054446--12054511 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 31
12054436 TCGTGATATA
*
12054446 AAAATAAAAAATAAAATAAATTTTTAGAAGT
1 AAAATAAAAAATAAAATAAATTATTAGAAGT
12054477 --AATAAAAAATAAAAT-AATTAATT-GAA-T
1 AAAATAAAAAATAAAATAAATT-ATTAGAAGT
12054504 AAAATAAA
1 AAAATAAA
12054512 TAATGACTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
27 1 0.03
28 7 0.23
29 23 0.74
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (31 bp):
AAAATAAAAAATAAAATAAATTATTAGAAGT
Found at i:12054737 original size:19 final size:19
Alignment explanation
Indices: 12054710--12054749 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
12054700 CCTAATCACA
*
12054710 AAACCCGAACC-CCAACCC
1 AAACCCGAACCACAAACCC
12054728 AAACCTCGAACCACAAACCC
1 AAACC-CGAACCACAAACCC
12054748 AA
1 AA
12054750 TCCCAGACCC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 5 0.26
19 6 0.32
20 8 0.42
ACGTcount: A:0.45, C:0.47, G:0.05, T:0.03
Consensus pattern (19 bp):
AAACCCGAACCACAAACCC
Found at i:12059109 original size:28 final size:28
Alignment explanation
Indices: 12059067--12059227 Score: 93
Period size: 28 Copynumber: 5.9 Consensus size: 28
12059057 GGCTAGTGGG
* *
12059067 TGAAGGTATTCATCTCCTTT-TGGTAGGT
1 TGAAAGTATTCATCT-ATTTATGGTAGGT
*
12059095 TGAAAGTATTTATCTATTTATGGTAGGT
1 TGAAAGTATTCATCTATTTATGGTAGGT
* * * *
12059123 T-ATAAGTATACATCCATTT-TTG-ATGT
1 TGA-AAGTATTCATCTATTTATGGTAGGT
* * * * **
12059149 T-AAGGTATCCATCTCCTTT-TGATAAAT
1 TGAAAGTATTCATCT-ATTTATGGTAGGT
12059176 TGAAAGTATTCATCTATTTATGGTAGGT
1 TGAAAGTATTCATCTATTTATGGTAGGT
* * *
12059204 T-ATAAGTATACATCCATTTTTGGT
1 TGA-AAGTATTCATCTATTTATGGT
12059228 GAGTGATCCA
Statistics
Matches: 101, Mismatches: 25, Indels: 14
0.72 0.18 0.10
Matches are distributed among these distances:
25 9 0.09
26 9 0.09
27 13 0.13
28 70 0.69
ACGTcount: A:0.27, C:0.11, G:0.17, T:0.44
Consensus pattern (28 bp):
TGAAAGTATTCATCTATTTATGGTAGGT
Found at i:12059179 original size:81 final size:81
Alignment explanation
Indices: 12059069--12059225 Score: 269
Period size: 81 Copynumber: 1.9 Consensus size: 81
12059059 CTAGTGGGTG
* * ** *
12059069 AAGGTATTCATCTCCTTTTGGTAGGTTGAAAGTATTTATCTATTTATGGTAGGTTATAAGTATAC
1 AAGGTATCCATCTCCTTTTGATAAATTGAAAGTATTCATCTATTTATGGTAGGTTATAAGTATAC
12059134 ATCCATTTTTGATGTT
66 ATCCATTTTTGATGTT
12059150 AAGGTATCCATCTCCTTTTGATAAATTGAAAGTATTCATCTATTTATGGTAGGTTATAAGTATAC
1 AAGGTATCCATCTCCTTTTGATAAATTGAAAGTATTCATCTATTTATGGTAGGTTATAAGTATAC
12059215 ATCCATTTTTG
66 ATCCATTTTTG
12059226 GTGAGTGATC
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
81 71 1.00
ACGTcount: A:0.28, C:0.11, G:0.17, T:0.44
Consensus pattern (81 bp):
AAGGTATCCATCTCCTTTTGATAAATTGAAAGTATTCATCTATTTATGGTAGGTTATAAGTATAC
ATCCATTTTTGATGTT
Found at i:12059582 original size:53 final size:53
Alignment explanation
Indices: 12059467--12059621 Score: 184
Period size: 53 Copynumber: 2.8 Consensus size: 53
12059457 AAATAATGTC
* * * *
12059467 ACATTCACTTCAGGGAATGGATAGATTTATAATTTTTTATTAATATCTCATTTGTT
1 ACATTCACTTCAAGGAAT-GA-ACATTCATAA-TTTTTATTAATAGCTCATTTGTT
* **
12059523 ACATTCACTTCAAGGAATGAACATTCATAATTTTTATTAGTAGCTTGTTTGTT
1 ACATTCACTTCAAGGAATGAACATTCATAATTTTTATTAATAGCTCATTTGTT
* **
12059576 ATATTCACTTCAAGGAATGAACATTCATGGTTTTTCATTAATAGCT
1 ACATTCACTTCAAGGAATGAACATTCATAATTTTT-ATTAATAGCT
12059622 ATATACTATC
Statistics
Matches: 87, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
53 51 0.59
54 17 0.20
55 2 0.02
56 17 0.20
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.43
Consensus pattern (53 bp):
ACATTCACTTCAAGGAATGAACATTCATAATTTTTATTAATAGCTCATTTGTT
Done.