Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1470
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: 123034
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:14170 original size:15 final size:14
Alignment explanation
Indices: 14150--14190 Score: 55
Period size: 15 Copynumber: 2.8 Consensus size: 14
14140 AGTCCATTTA
14150 TTTTATTTTTTTATT
1 TTTTATTTTTTT-TT
14165 TTTTATTTTTGTTTT
1 TTTTATTTTT-TTTT
*
14180 ATTTATTTTTT
1 TTTTATTTTTT
14191 GAAACTTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 1 0.04
15 21 0.88
16 2 0.08
ACGTcount: A:0.12, C:0.00, G:0.02, T:0.85
Consensus pattern (14 bp):
TTTTATTTTTTTTT
Found at i:24688 original size:8 final size:8
Alignment explanation
Indices: 24675--24700 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
24665 TATGCCTTTA
24675 TTTTTATT
1 TTTTTATT
24683 TTTTTATT
1 TTTTTATT
24691 TTTTTATT
1 TTTTTATT
24699 TT
1 TT
24701 ATTACTTTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTTTATT
Found at i:27333 original size:12 final size:12
Alignment explanation
Indices: 27318--27368 Score: 59
Period size: 12 Copynumber: 4.2 Consensus size: 12
27308 AAAAGTAATT
*
27318 TAAAAATATAAA
1 TAAAAATAAAAA
*
27330 TAAAGATAAAAA
1 TAAAAATAAAAA
27342 T-AAAATAAAAAA
1 TAAAAAT-AAAAA
27354 TAAAAATAAATAA
1 TAAAAATAAA-AA
27367 TA
1 TA
27369 GATGTTTATA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
11 4 0.12
12 20 0.61
13 9 0.27
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (12 bp):
TAAAAATAAAAA
Found at i:27339 original size:18 final size:18
Alignment explanation
Indices: 27318--27363 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
27308 AAAAGTAATT
*
27318 TAAAAATATAAAT-AAAGA
1 TAAAAATA-AAATAAAAAA
27336 TAAAAATAAAATAAAAAA
1 TAAAAATAAAATAAAAAA
27354 TAAAAATAAA
1 TAAAAATAAA
27364 TAATAGATGT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 4 0.15
18 22 0.85
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (18 bp):
TAAAAATAAAATAAAAAA
Found at i:33278 original size:12 final size:13
Alignment explanation
Indices: 33258--33290 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
33248 AATATATGTA
33258 AAATTGAAG-TTT
1 AAATTGAAGCTTT
*
33270 AATTTGAAGCTTT
1 AAATTGAAGCTTT
33283 AAATTGAA
1 AAATTGAA
33291 AGTTATGGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 8 0.44
13 10 0.56
ACGTcount: A:0.42, C:0.03, G:0.15, T:0.39
Consensus pattern (13 bp):
AAATTGAAGCTTT
Found at i:33954 original size:19 final size:19
Alignment explanation
Indices: 33904--33960 Score: 60
Period size: 19 Copynumber: 3.0 Consensus size: 19
33894 GTGTGCTGGA
*
33904 TATGTGCTTTGTGTGCTAG
1 TATGTGCTTTGTGTGCCAG
* **
33923 AATGCACTTTGTGTGCCAG
1 TATGTGCTTTGTGTGCCAG
* *
33942 TATGTGCTATGTGCGCCAG
1 TATGTGCTTTGTGTGCCAG
33961 GATGCATTTT
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.16, C:0.18, G:0.30, T:0.37
Consensus pattern (19 bp):
TATGTGCTTTGTGTGCCAG
Found at i:40037 original size:10 final size:9
Alignment explanation
Indices: 39985--40107 Score: 73
Period size: 10 Copynumber: 13.7 Consensus size: 9
39975 ATATTTTTTC
39985 ATAAAAATT
1 ATAAAAATT
39994 ATTAAAAA-T
1 A-TAAAAATT
*
40003 AAAAAAATT
1 ATAAAAATT
40012 AT--AAATT
1 ATAAAAATT
*
40019 GATATAAATAT
1 -ATAAAAAT-T
*
40030 ATAAAAATC
1 ATAAAAATT
40039 ATAAAAATTT
1 ATAAAAA-TT
*
40049 ATAAATATT
1 ATAAAAATT
40058 ATAAAAA--
1 ATAAAAATT
40065 AT-AAAATT
1 ATAAAAATT
40073 CA-AATAAATT
1 -ATAA-AAATT
*
40083 TTAAAAAATT
1 AT-AAAAATT
40093 AT-AAAATT
1 ATAAAAATT
40101 AGTAAAA
1 A-TAAAA
40108 CATATTTTAA
Statistics
Matches: 89, Mismatches: 9, Indels: 31
0.69 0.07 0.24
Matches are distributed among these distances:
6 4 0.04
7 7 0.08
8 14 0.16
9 23 0.26
10 38 0.43
11 3 0.03
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (9 bp):
ATAAAAATT
Found at i:40051 original size:19 final size:19
Alignment explanation
Indices: 39983--40064 Score: 64
Period size: 19 Copynumber: 4.5 Consensus size: 19
39973 TTATATTTTT
39983 TCATAAAAA-TTATTAAAAA
1 TCATAAAAATTTA-TAAAAA
* *
40002 T-A-AAAAAATTAT-AAAT
1 TCATAAAAATTTATAAAAA
* * *
40018 TGATATAAATATATAAAAA
1 TCATAAAAATTTATAAAAA
*
40037 TCATAAAAATTTATAAATA
1 TCATAAAAATTTATAAAAA
*
40056 TTATAAAAA
1 TCATAAAAA
40065 ATAAAATTCA
Statistics
Matches: 49, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
16 4 0.08
17 7 0.14
18 11 0.22
19 27 0.55
ACGTcount: A:0.63, C:0.02, G:0.01, T:0.33
Consensus pattern (19 bp):
TCATAAAAATTTATAAAAA
Found at i:40051 original size:27 final size:27
Alignment explanation
Indices: 39983--40064 Score: 80
Period size: 27 Copynumber: 3.0 Consensus size: 27
39973 TTATATTTTT
* *
39983 TCATAAAAA-TTATTAAAAATAAAAAAA
1 TCATAAAAATTTA-TAAATATATAAAAA
*
40010 T--TATAAATTGATATAAATATATAAAAA
1 TCATAAAAATT--TATAAATATATAAAAA
40037 TCATAAAAATTTATAAATATTATAAAAA
1 TCATAAAAATTTATAAATA-TATAAAAA
40065 ATAAAATTCA
Statistics
Matches: 45, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
25 5 0.11
26 1 0.02
27 22 0.49
28 10 0.22
29 7 0.16
ACGTcount: A:0.63, C:0.02, G:0.01, T:0.33
Consensus pattern (27 bp):
TCATAAAAATTTATAAATATATAAAAA
Found at i:40069 original size:35 final size:34
Alignment explanation
Indices: 39996--40098 Score: 95
Period size: 35 Copynumber: 2.9 Consensus size: 34
39986 TAAAAATTAT
* *
39996 TAAAAAT-AAAAAAATTATAAAT-TGATATAAATATA
1 TAAAAATCAAAAAATTTATAAATAT--TATAAA-AAA
40031 TAAAAATCATAAAAATTTATAAATATTATAAAAAA
1 TAAAAATCA-AAAAATTTATAAATATTATAAAAAA
* *
40066 TAAAATTCAAATAAATTT-TAAAAAATTATAAAA
1 TAAAAATCAAA-AAATTTAT-AAATATTATAAAA
40099 TTAGTAAAAC
Statistics
Matches: 59, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
34 3 0.05
35 35 0.59
36 7 0.12
37 13 0.22
38 1 0.02
ACGTcount: A:0.65, C:0.02, G:0.01, T:0.32
Consensus pattern (34 bp):
TAAAAATCAAAAAATTTATAAATATTATAAAAAA
Found at i:40072 original size:54 final size:54
Alignment explanation
Indices: 39983--40107 Score: 125
Period size: 54 Copynumber: 2.3 Consensus size: 54
39973 TTATATTTTT
* *
39983 TCATAAAAATTATTAAAAATAAAAAAATTATAAATTGATATAAA-TATATAAAAA
1 TCATAAAAATTATTAAAAATAAAAAAATTATAAATTCAAATAAATTATA-AAAAA
* *
40037 TCATAAAAATT-TATAAATATTATAAAAAA-TA-AAATTCAAATAAATTTTAAAAAA
1 TCATAAAAATTAT-TAAA-AATA-AAAAAATTATAAATTCAAATAAATTATAAAAAA
* *
40091 TTAT-AAAATTAGTAAAA
1 TCATAAAAATTATTAAAA
40108 CATATTTTAA
Statistics
Matches: 60, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
52 1 0.02
53 11 0.18
54 34 0.57
55 8 0.13
56 6 0.10
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (54 bp):
TCATAAAAATTATTAAAAATAAAAAAATTATAAATTCAAATAAATTATAAAAAA
Found at i:41184 original size:26 final size:22
Alignment explanation
Indices: 41132--41175 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
41122 TATTATAGAG
41132 TTAAATTAATTCATGGTCCAAT
1 TTAAATTAATTCATGGTCCAAT
41154 TTAAATTAATTCATGGTCCAAT
1 TTAAATTAATTCATGGTCCAAT
41176 CATTTTAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (22 bp):
TTAAATTAATTCATGGTCCAAT
Found at i:49000 original size:10 final size:9
Alignment explanation
Indices: 48971--49079 Score: 71
Period size: 10 Copynumber: 11.7 Consensus size: 9
48961 ATTTTATTCA
48971 TTTTATAAT
1 TTTTATAAT
* *
48980 TTATAAGAAT
1 TT-TTATAAT
48990 TTTTATTAAT
1 TTTTA-TAAT
49000 TTTTATAAGT
1 TTTTATAA-T
49010 TTTTATAATT
1 TTTTATAA-T
49020 TTTTATAAT
1 TTTTATAAT
* *
49029 TATTGTAAGT
1 TTTTATAA-T
* *
49039 TTATGTCAA-
1 TTTTAT-AAT
49048 TTTTACT-AT
1 TTTTA-TAAT
*
49057 TTTTA-ATT
1 TTTTATAAT
49065 TTTTATAAT
1 TTTTATAAT
49074 TTTTAT
1 TTTTAT
49080 GAGAAAATAC
Statistics
Matches: 78, Mismatches: 13, Indels: 18
0.72 0.12 0.17
Matches are distributed among these distances:
8 7 0.09
9 30 0.38
10 39 0.50
11 2 0.03
ACGTcount: A:0.31, C:0.02, G:0.05, T:0.62
Consensus pattern (9 bp):
TTTTATAAT
Found at i:49078 original size:9 final size:9
Alignment explanation
Indices: 48870--49079 Score: 87
Period size: 9 Copynumber: 22.8 Consensus size: 9
48860 GGTTTAAATT
48870 TTTTTATAA
1 TTTTTATAA
48879 --TTTATAA
1 TTTTTATAA
**
48886 TTTTCCTAA
1 TTTTTATAA
48895 TTTATTATAA
1 TTT-TTATAA
* *
48905 TTTTGAT-G
1 TTTTTATAA
48913 TTATTTATAA
1 TT-TTTATAA
48923 GTTTTTATGAA
1 -TTTTTAT-AA
*
48934 TTCTTATAA
1 TTTTTATAA
**
48943 AATTTA-AA
1 TTTTTATAA
*
48951 TATTGTAT-A
1 T-TTTTATAA
*
48960 TATTTTATTCA
1 T-TTTTA-TAA
48971 -TTTTATAA
1 TTTTTATAA
* *
48979 TTTATAAGAA
1 TTT-TTATAA
48989 TTTTTATTAA
1 TTTTTA-TAA
48999 TTTTTATAA
1 TTTTTATAA
49008 GTTTTTATAA
1 -TTTTTATAA
49018 TTTTTTATAA
1 -TTTTTATAA
* *
49028 TTATTGTAA
1 TTTTTATAA
* *
49037 GTTTATGTCAA
1 -TTTTTAT-AA
49048 -TTTTACT-A
1 TTTTTA-TAA
*
49056 TTTTTA-AT
1 TTTTTATAA
49064 TTTTTATAA
1 TTTTTATAA
49073 TTTTTAT
1 TTTTTAT
49080 GAGAAAATAC
Statistics
Matches: 150, Mismatches: 30, Indels: 42
0.68 0.14 0.19
Matches are distributed among these distances:
7 7 0.05
8 13 0.09
9 65 0.43
10 58 0.39
11 7 0.05
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.60
Consensus pattern (9 bp):
TTTTTATAA
Found at i:49606 original size:18 final size:18
Alignment explanation
Indices: 49570--49607 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
49560 TGAGTTTTAC
*
49570 AATTCAAATACTTCGAAT
1 AATTCAAATACTTCAAAT
49588 AATTCAAATAACTT-AAAT
1 AATTCAAAT-ACTTCAAAT
49606 AA
1 AA
49608 CATATTAGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.53, C:0.13, G:0.03, T:0.32
Consensus pattern (18 bp):
AATTCAAATACTTCAAAT
Found at i:49733 original size:19 final size:20
Alignment explanation
Indices: 49690--49743 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
49680 CAACCAAAAT
49690 AATTCAAAATAATTT-TCAAA
1 AATTCAAAAT-ATTTATCAAA
*
49710 TATTCAAAATATTTAT-AAA
1 AATTCAAAATATTTATCAAA
49729 AATTCCAAAAT-TTTA
1 AATT-CAAAATATTTA
49744 AATTTTTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (20 bp):
AATTCAAAATATTTATCAAA
Found at i:49784 original size:10 final size:9
Alignment explanation
Indices: 49769--49820 Score: 52
Period size: 11 Copynumber: 5.3 Consensus size: 9
49759 ATGAAAAATT
49769 AAAAATTCTA
1 AAAAATT-TA
49779 AAAAATTT-
1 AAAAATTTA
49787 AAAAATGTATA
1 AAAAAT-T-TA
49798 AAAAATGTTTA
1 AAAAA--TTTA
49809 AAAAATTTA
1 AAAAATTTA
49818 AAA
1 AAA
49821 TATAAAACAA
Statistics
Matches: 37, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
8 6 0.16
9 9 0.24
10 8 0.22
11 12 0.32
12 1 0.03
13 1 0.03
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (9 bp):
AAAAATTTA
Found at i:49788 original size:18 final size:19
Alignment explanation
Indices: 49762--49803 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
49752 ATAAAATATG
*
49762 AAAAA-TTAAAAAT-TCTA
1 AAAAATTTAAAAATGTATA
49779 AAAAATTTAAAAATGTATA
1 AAAAATTTAAAAATGTATA
49798 AAAAAT
1 AAAAAT
49804 GTTTAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.23
18 8 0.36
19 9 0.41
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (19 bp):
AAAAATTTAAAAATGTATA
Found at i:50838 original size:3 final size:3
Alignment explanation
Indices: 50830--50870 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
50820 ATTTATTTAT
50830 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
50871 TTGCTAGTGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:52273 original size:5 final size:5
Alignment explanation
Indices: 52256--52287 Score: 55
Period size: 5 Copynumber: 6.2 Consensus size: 5
52246 AAAAATGGTA
52256 GGCCC GAGCCC GGCCC GGCCC GGCCC GGCCC G
1 GGCCC G-GCCC GGCCC GGCCC GGCCC GGCCC G
52288 ATCATATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.03, C:0.56, G:0.41, T:0.00
Consensus pattern (5 bp):
GGCCC
Found at i:52359 original size:25 final size:23
Alignment explanation
Indices: 52330--52394 Score: 75
Period size: 19 Copynumber: 2.9 Consensus size: 23
52320 AATAAAAAAC
*
52330 TTTAAAATATAATAAATCAAATACA
1 TTTAAAACATAA-AAAT-AAATACA
52355 TTTAAAACATAAAAATAAATA-A
1 TTTAAAACATAAAAATAAATACA
52377 --TAAAACA-AAAAATAAATA
1 TTTAAAACATAAAAATAAATA
52395 AATAATGGGA
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
19 11 0.28
20 7 0.18
22 1 0.03
23 5 0.13
24 4 0.10
25 11 0.28
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (23 bp):
TTTAAAACATAAAAATAAATACA
Found at i:52671 original size:20 final size:21
Alignment explanation
Indices: 52622--52675 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 21
52612 ATATTAAAAT
*
52622 CGGGCCTCATTTTTTGTCCAA
1 CGGGCCTCATTTTTTGTCAAA
52643 ---GCC-CATTTTTTGT-AAA
1 CGGGCCTCATTTTTTGTCAAA
52659 CGGGCCTCATTTTTTGT
1 CGGGCCTCATTTTTTGT
52676 TAAAATTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 9
0.74 0.03 0.24
Matches are distributed among these distances:
16 2 0.07
17 10 0.36
18 3 0.11
19 3 0.11
20 10 0.36
ACGTcount: A:0.15, C:0.24, G:0.19, T:0.43
Consensus pattern (21 bp):
CGGGCCTCATTTTTTGTCAAA
Found at i:56148 original size:13 final size:13
Alignment explanation
Indices: 56112--56149 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
56102 AACCCTAATA
*
56112 AAAGAGAAAAACT
1 AAAGAGAAAATCT
*
56125 AAAGACAAAATCT
1 AAAGAGAAAATCT
56138 AAAGAGAAAATC
1 AAAGAGAAAATC
56150 ATACAAGGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.66, C:0.11, G:0.13, T:0.11
Consensus pattern (13 bp):
AAAGAGAAAATCT
Found at i:59469 original size:26 final size:26
Alignment explanation
Indices: 59440--59491 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
59430 AAATTACTAT
59440 GGTTTCCTTGGGAGTGATATAGAATC
1 GGTTTCCTTGGGAGTGATATAGAATC
59466 GGTTTCCTTGGGAGTGATATAGAATC
1 GGTTTCCTTGGGAGTGATATAGAATC
59492 ATTCCCAATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.23, C:0.12, G:0.31, T:0.35
Consensus pattern (26 bp):
GGTTTCCTTGGGAGTGATATAGAATC
Found at i:59935 original size:19 final size:19
Alignment explanation
Indices: 59907--59944 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
59897 TAGAGAATAG
*
59907 TAAAGAGGTTTTAGTAGTT
1 TAAAGAGGTTTTAATAGTT
*
59926 TAAAGTGGTTTTAATAGTT
1 TAAAGAGGTTTTAATAGTT
59945 GAGTAAAAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.24, T:0.45
Consensus pattern (19 bp):
TAAAGAGGTTTTAATAGTT
Found at i:59951 original size:22 final size:21
Alignment explanation
Indices: 59904--59960 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 21
59894 AGGTAGAGAA
* *
59904 TAGTAAAGAGGTTTTAGTAGT
1 TAGTAAAGTGGTTTTAATAGT
59925 T--TAAAGTGGTTTTAATAGT
1 TAGTAAAGTGGTTTTAATAGT
*
59944 TGAGTAAAAGTGTTTTT
1 T-AGT-AAAGTGGTTTT
59961 GAGTTAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
19 17 0.59
21 1 0.03
22 1 0.03
23 10 0.34
ACGTcount: A:0.32, C:0.00, G:0.25, T:0.44
Consensus pattern (21 bp):
TAGTAAAGTGGTTTTAATAGT
Found at i:62472 original size:18 final size:18
Alignment explanation
Indices: 62449--62483 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
62439 CTCATGGATC
62449 TGATAAACAAAATAAACT
1 TGATAAACAAAATAAACT
* *
62467 TGATAAAGATAATAAAC
1 TGATAAACAAAATAAAC
62484 GTAAAGAGCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.60, C:0.09, G:0.09, T:0.23
Consensus pattern (18 bp):
TGATAAACAAAATAAACT
Found at i:64071 original size:25 final size:25
Alignment explanation
Indices: 64043--64110 Score: 75
Period size: 25 Copynumber: 2.7 Consensus size: 25
64033 CTTTTTAGAT
* *
64043 TTAGTTTTTAGTTTTTTTTCTTTTC
1 TTAGTTTTTAGTTTTATTTCTATTC
*
64068 TTAGGTTTTAGATTTTATTTCTATTC
1 TTAGTTTTTAG-TTTTATTTCTATTC
*
64094 TT-GTTATTTACTTTTAT
1 TTAGTT-TTTAGTTTTAT
64111 GGAGAAATCA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
25 18 0.50
26 18 0.50
ACGTcount: A:0.15, C:0.07, G:0.09, T:0.69
Consensus pattern (25 bp):
TTAGTTTTTAGTTTTATTTCTATTC
Found at i:64075 original size:26 final size:26
Alignment explanation
Indices: 64043--64095 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
64033 CTTTTTAGAT
* * *
64043 TTAGTTTTTAG-TTTTTTTTCTTTTC
1 TTAGGTTTTAGATTTTATTTCTATTC
64068 TTAGGTTTTAGATTTTATTTCTATTC
1 TTAGGTTTTAGATTTTATTTCTATTC
64094 TT
1 TT
64096 GTTATTTACT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
25 10 0.42
26 14 0.58
ACGTcount: A:0.13, C:0.08, G:0.09, T:0.70
Consensus pattern (26 bp):
TTAGGTTTTAGATTTTATTTCTATTC
Found at i:76088 original size:46 final size:47
Alignment explanation
Indices: 76018--76188 Score: 174
Period size: 46 Copynumber: 3.7 Consensus size: 47
76008 AACCCGCCCC
* *
76018 TAAGTGAACTCAGACTCAACTCAACGAGCTCGAG-CGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGAGACGTTCGCATCCA
* * * *
76064 TAAGTGAACTCGGACTCAAGTCAACGAGTTCAGATGCCTAGTT-ACAT--T
1 TAAGTGAACTCGGACTCAACTCAACGAGTTC-GA-GAC--GTTCGCATCCA
* * * *
76112 TCA-CGAACTCGAACTCAACTCAACGAGTTCG-GACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGAGACGTTCGCATCCA
76157 TAAGTGAACTCGGACTCAACTCAACGAGTTCG
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCG
76189 GATGCTCAAC
Statistics
Matches: 100, Mismatches: 16, Indels: 18
0.75 0.12 0.13
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 2 0.02
45 2 0.02
46 55 0.55
47 26 0.26
48 3 0.03
49 1 0.01
50 3 0.03
51 3 0.03
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.22
Consensus pattern (47 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGAGACGTTCGCATCCA
Found at i:76136 original size:93 final size:93
Alignment explanation
Indices: 76023--76193 Score: 274
Period size: 93 Copynumber: 1.8 Consensus size: 93
76013 GCCCCTAAGT
* *
76023 GAACTCAGACTCAACTCAACGAGCTC-GAGCGTTCGCATCCATAAGTGAACTCGGACTCAAGTCA
1 GAACTCAGACTCAACTCAACGAGCTCGGA-CATTCGCATCCATAAGTGAACTCGGACTCAACTCA
76087 ACGAGTTCAGATGCCTAGTTACATTTCAC
65 ACGAGTTCAGATGCCTAGTTACATTTCAC
*
76116 GAACTC-GAACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 GAACTCAG-ACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
*
76180 ACGAGTTCGGATGC
65 ACGAGTTCAGATGC
76194 TCAACCATCC
Statistics
Matches: 72, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
92 1 0.01
93 69 0.96
94 2 0.03
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (93 bp):
GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCAGATGCCTAGTTACATTTCAC
Found at i:76209 original size:46 final size:45
Alignment explanation
Indices: 76116--76201 Score: 120
Period size: 46 Copynumber: 1.9 Consensus size: 45
76106 TACATTTCAC
* *
76116 GAACTCGAACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGT
1 GAACTCGAACTCAACTCAACGAGTTCGGA-ATGCGCAACCATAAGT
* *
76162 GAACTCGGACTCAACTCAACGAGTTCGG-ATGCTCAACCAT
1 GAACTCGAACTCAACTCAACGAGTTCGGAATGCGCAACCAT
76202 CCTAGTGACA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
44 9 0.25
46 27 0.75
ACGTcount: A:0.31, C:0.29, G:0.19, T:0.21
Consensus pattern (45 bp):
GAACTCGAACTCAACTCAACGAGTTCGGAATGCGCAACCATAAGT
Found at i:76646 original size:30 final size:30
Alignment explanation
Indices: 76612--76672 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
76602 CATTTAATAC
76612 AAACTTTGGAAAAATTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACACTTTTGCCCCT
* * *
76642 AAACTTTTGCATAATTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACACTTTTGCCCCT
76672 A
1 A
76673 GGCTCGGGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.31, C:0.25, G:0.08, T:0.36
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACACTTTTGCCCCT
Found at i:90749 original size:11 final size:11
Alignment explanation
Indices: 90733--90757 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
90723 TTTTGTCCCC
90733 TTTTGGCTCAT
1 TTTTGGCTCAT
90744 TTTTGGCTCAT
1 TTTTGGCTCAT
90755 TTT
1 TTT
90758 AACTCTTGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.16, G:0.16, T:0.60
Consensus pattern (11 bp):
TTTTGGCTCAT
Found at i:93640 original size:15 final size:15
Alignment explanation
Indices: 93620--93652 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
93610 AAATATATAT
93620 TTTATA-AAAAATTAA
1 TTTATATAAAAA-TAA
93635 TTTATATAAAAATAA
1 TTTATATAAAAATAA
93650 TTT
1 TTT
93653 GATTCCTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TTTATATAAAAATAA
Found at i:95784 original size:18 final size:17
Alignment explanation
Indices: 95746--95804 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 17
95736 AATTTAAGAT
*
95746 TTTTATGCTTTTTTTTCA
1 TTTTATGATTTTTTTT-A
95764 TTTTA-GAATTTTTTTGTA
1 TTTTATG-ATTTTTTT-TA
95782 TTTTTATGATTTTTTTATA
1 -TTTTATGATTTTTTT-TA
95801 TTTT
1 TTTT
95805 TTAAGGAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
17 1 0.03
18 17 0.49
19 16 0.46
20 1 0.03
ACGTcount: A:0.17, C:0.03, G:0.07, T:0.73
Consensus pattern (17 bp):
TTTTATGATTTTTTTTA
Found at i:95786 original size:19 final size:19
Alignment explanation
Indices: 95744--95805 Score: 67
Period size: 19 Copynumber: 3.3 Consensus size: 19
95734 AAAATTTAAG
*
95744 ATTTTTATGCTTTTTTT-T
1 ATTTTTATGATTTTTTTAT
*
95762 CA-TTTTA-GAATTTTTTTGT
1 -ATTTTTATG-ATTTTTTTAT
95781 ATTTTTATGATTTTTTTAT
1 ATTTTTATGATTTTTTTAT
95800 ATTTTT
1 ATTTTT
95806 TAAGGAATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
17 1 0.03
18 13 0.35
19 22 0.59
20 1 0.03
ACGTcount: A:0.18, C:0.03, G:0.06, T:0.73
Consensus pattern (19 bp):
ATTTTTATGATTTTTTTAT
Found at i:96778 original size:16 final size:17
Alignment explanation
Indices: 96759--96791 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
96749 ATAATTACTT
96759 TTTAT-TATATTTTTAA
1 TTTATGTATATTTTTAA
*
96775 TTTATGTATTTTTTTAA
1 TTTATGTATATTTTTAA
96792 GAATTATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (17 bp):
TTTATGTATATTTTTAA
Found at i:100030 original size:99 final size:101
Alignment explanation
Indices: 99669--100092 Score: 584
Period size: 99 Copynumber: 4.2 Consensus size: 101
99659 TGGTTTAATG
* * * * * * * *
99669 TTTTTTATAAATGTAATTTTTTTATAATTATTTTAAAATTTTTTTTGTTAGTAGTTTATGATTAT
1 TTTTTTATTAATGTAATTTTTTAAAAATTATTTT-ATAGTTATTTTGTTAGTAATTTATGATTAG
* * *
99734 GTTGTAATTTGTTTGTGTTTTAGTTTAGTGTTTTGTGA
65 GTTATAAATTGTTAGTG-TTTAGTTTAGTGTTTTGTGA
* *
99772 ATTTTTATTAATGTAATTTTTTAAAAAAATTTATTTTATAGTTATTTTGTTAATAATTTATGATT
1 TTTTTTATTAATGTAATTTTTT--AAAAA-TTATTTTATAGTTATTTTGTTAGTAATTTATGATT
*
99837 AGGTTATAAATTGTT-CTGTTTAGTTTAGTGTTTTGTGA
63 AGGTTATAAATTGTTAGTGTTTAGTTTAGTGTTTTGTGA
* *
99875 TTTTTTTATTAATGCAAATTTTTTAAAAAATATTTTATAGTTATTTTGTTAGTAATTTATGATTA
1 -TTTTTTATTAATG-TAATTTTTTAAAAATTATTTTATAGTTATTTTGTTAGTAATTTATGATTA
* *
99940 GGTTATAAATTGTTAGTGTTTAGTTTTGTATTTTGTGA
64 GGTTATAAATTGTTAGTGTTTAGTTTAGTGTTTTGTGA
99978 -TTTTTATTAATGTAATTTTTT-AAAATTATTTTATAGTTATTTTGTTAGTAATTTATGATTAGG
1 TTTTTTATTAATGTAATTTTTTAAAAATTATTTTATAGTTATTTTGTTAGTAATTTATGATTAGG
* *
100041 TTATAAATTGTTAGTGTTTAGTTTACTGTTTTTTGA
66 TTATAAATTGTTAGTGTTTAGTTTAGTGTTTTGTGA
100077 TTTTTTATTAATGTAA
1 TTTTTTATTAATGTAA
100093 AATTTTTATA
Statistics
Matches: 288, Mismatches: 26, Indels: 17
0.87 0.08 0.05
Matches are distributed among these distances:
99 73 0.25
100 23 0.08
101 12 0.04
102 48 0.17
103 65 0.23
104 14 0.05
105 46 0.16
106 7 0.02
ACGTcount: A:0.28, C:0.01, G:0.13, T:0.58
Consensus pattern (101 bp):
TTTTTTATTAATGTAATTTTTTAAAAATTATTTTATAGTTATTTTGTTAGTAATTTATGATTAGG
TTATAAATTGTTAGTGTTTAGTTTAGTGTTTTGTGA
Found at i:100122 original size:201 final size:203
Alignment explanation
Indices: 99669--100122 Score: 614
Period size: 201 Copynumber: 2.2 Consensus size: 203
99659 TGGTTTAATG
* * *
99669 TTTTTTATAAATGTAATTTTTTTATAATTATTTTAAAATTTT-TTTTGTTAGTAGTTTATGATTA
1 TTTTTTATTAATGTAAATTTTTTATAATTATTTT---ATTTTATTTTGTTAGTAATTTATGATTA
* * * * *
99733 TGTTGTAATTTGTTTGTGTTTTAGTTTAGTGTTTTGTGAATTTTTATTAATGTAATTTTTTAAAA
63 GGTTATAAATTGTTAGTGTTTTAGTTTAGTATTTTGTGAATTTTTATTAATGTAATTTTTT--AA
99798 AAATTTATTTTATAGTTATTTTGTTAATAATTTATGATTAGGTTATAAATTGTTCTGTTTAGTTT
126 AAATTTATTTTATAGTTATTTTGTTAATAATTTATGATTAGGTTATAAATTGTTCTGTTTAGTTT
*
99863 AGTGTTTTGTGAT
191 ACTGTTTTGTGAT
* * * *
99876 TTTTTTATTAATGCAAATTTTTTAAAAAATATTTTATAGTTATTTTGTTAGTAATTTATGATTAG
1 TTTTTTATTAATGTAAATTTTTT-ATAATTATTTTAT-TTTATTTTGTTAGTAATTTATGATTAG
*
99941 GTTATAAATTGTTAGTG-TTTAGTTTTGTATTTTGTG-ATTTTTATTAATGTAATTTTTT-AAAA
64 GTTATAAATTGTTAGTGTTTTAGTTTAGTATTTTGTGAATTTTTATTAATGTAATTTTTTAAAAA
* *
100003 -TTATTTTATAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAATTGTTAGTGTTTAGTTTAC
129 TTTATTTTATAGTTATTTTGTTAATAATTTATGATTAGGTTATAAATTGTT-CTGTTTAGTTTAC
*
100067 TGTTTTTTGA-
193 TGTTTTGTGAT
*
100077 TTTTTTATTAATGTAAAATTTTTATAATGTAATTTTATTTTATTTT
1 TTTTTTATTAATGTAAATTTTTTATAAT-T-ATTTTATTTTATTTT
100123 TATTTATTTG
Statistics
Matches: 219, Mismatches: 22, Indels: 18
0.85 0.08 0.07
Matches are distributed among these distances:
200 3 0.01
201 78 0.36
202 31 0.14
205 24 0.11
206 19 0.09
207 55 0.25
208 9 0.04
ACGTcount: A:0.28, C:0.01, G:0.13, T:0.59
Consensus pattern (203 bp):
TTTTTTATTAATGTAAATTTTTTATAATTATTTTATTTTATTTTGTTAGTAATTTATGATTAGGT
TATAAATTGTTAGTGTTTTAGTTTAGTATTTTGTGAATTTTTATTAATGTAATTTTTTAAAAATT
TATTTTATAGTTATTTTGTTAATAATTTATGATTAGGTTATAAATTGTTCTGTTTAGTTTACTGT
TTTGTGAT
Found at i:105747 original size:18 final size:17
Alignment explanation
Indices: 105712--105747 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
105702 AACACCTTAT
*
105712 CTTTCTTTTTTGTTCTC
1 CTTTCTTTTTTCTTCTC
105729 CTTTCTTTCTTTCTTCTC
1 CTTTCTTT-TTTCTTCTC
105747 C
1 C
105748 CTATCTTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.00, C:0.31, G:0.03, T:0.67
Consensus pattern (17 bp):
CTTTCTTTTTTCTTCTC
Found at i:110800 original size:17 final size:17
Alignment explanation
Indices: 110769--110825 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 17
110759 TAATAAATTT
*
110769 AAAATATAATATATAATA
1 AAAATAT-ATTTATAATA
*
110787 AAAATATATTTATAAGA
1 AAAATATATTTATAATA
*
110804 ATAATA-A-TTAT-ATA
1 AAAATATATTTATAATA
110818 AAAATATA
1 AAAATATA
110826 AAATATATTG
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
14 7 0.21
15 5 0.15
16 1 0.03
17 13 0.39
18 7 0.21
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (17 bp):
AAAATATATTTATAATA
Found at i:111361 original size:17 final size:18
Alignment explanation
Indices: 111308--111405 Score: 137
Period size: 18 Copynumber: 5.5 Consensus size: 18
111298 AATCATATCT
*
111308 TCTAAGATTGTATATCATA
1 TCTAAGATTG-CTATCATA
*
111327 TCTAAGATTGCAATCATA
1 TCTAAGATTGCTATCATA
111345 TCTAAGATTG-TATCATA
1 TCTAAGATTGCTATCATA
*
111362 TCTAAGATTGCAATCATA
1 TCTAAGATTGCTATCATA
*
111380 TTTAAGATTG-TATCATA
1 TCTAAGATTGCTATCATA
111397 TCTAAGATT
1 TCTAAGATT
111406 ACATATCATT
Statistics
Matches: 71, Mismatches: 7, Indels: 4
0.87 0.09 0.05
Matches are distributed among these distances:
17 30 0.42
18 31 0.44
19 10 0.14
ACGTcount: A:0.37, C:0.12, G:0.11, T:0.40
Consensus pattern (18 bp):
TCTAAGATTGCTATCATA
Found at i:111366 original size:35 final size:35
Alignment explanation
Indices: 111308--111414 Score: 169
Period size: 35 Copynumber: 3.0 Consensus size: 35
111298 AATCATATCT
111308 TCTAAGATTGTATATCATATCTAAGATTGCAATCATA
1 TCTAAGATTG--TATCATATCTAAGATTGCAATCATA
111345 TCTAAGATTGTATCATATCTAAGATTGCAATCATA
1 TCTAAGATTGTATCATATCTAAGATTGCAATCATA
* *
111380 TTTAAGATTGTATCATATCTAAGATTACATATCAT
1 TCTAAGATTGTATCATATCTAAGATTGCA-ATCAT
111415 TGAAGATTAT
Statistics
Matches: 67, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
35 52 0.78
36 5 0.07
37 10 0.15
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.39
Consensus pattern (35 bp):
TCTAAGATTGTATCATATCTAAGATTGCAATCATA
Found at i:111983 original size:83 final size:83
Alignment explanation
Indices: 111812--112150 Score: 572
Period size: 83 Copynumber: 4.1 Consensus size: 83
111802 GATGTCAAGT
* * *
111812 CATCTTGAGTCTGTTTGA-AACATTTGAGAATCATATCTGCAAGGTCCTGGACTTGTTCCTTGTA
1 CATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAAGGTCCTCGATTTGTTCCTTGTA
111876 AGCACAAGGATGCCTAAAC
66 AGCACAAGGATGCC-AAAC
*
111895 CATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATGTCTGCAAGGTCCTCGATTTGTTCCTTGTA
1 CATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAAGGTCCTCGATTTGTTCCTTGTA
*
111960 AGCACAAGGATGCTAAAC
66 AGCACAAGGATGCCAAAC
* *
111978 CATCTTGAGTCTGTTTGAGGACATTTGAGAGTCATATCTGCAATGTCCTCGATTTGTTCCTTGTA
1 CATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAAGGTCCTCGATTTGTTCCTTGTA
*
112043 AGCACAAGGATACCAAAC
66 AGCACAAGGATGCCAAAC
* *
112061 CATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAATGTCCTTGATTTGTTCCTTGTA
1 CATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAAGGTCCTCGATTTGTTCCTTGTA
112126 AGCACAAGGATGCCAAAC
66 AGCACAAGGATGCCAAAC
112144 CATCTTG
1 CATCTTG
112151 GATCTGCTTC
Statistics
Matches: 242, Mismatches: 13, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
83 187 0.77
84 55 0.23
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33
Consensus pattern (83 bp):
CATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAAGGTCCTCGATTTGTTCCTTGTA
AGCACAAGGATGCCAAAC
Found at i:112285 original size:119 final size:119
Alignment explanation
Indices: 112074--112553 Score: 793
Period size: 119 Copynumber: 4.0 Consensus size: 119
112064 CTTGAGTCTG
* * * * * * *
112074 TTTGAGAACATTTGAGAGTCATATCTGCAATGTCCTTGATTTGTTCCTTGTAAGCACAAGGATGC
1 TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATGC
*
112139 CAAACCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATA
66 CAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATA
*
112193 TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATAC
1 TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATGC
* *
112258 CAAATCATCTTAGATATGCTTCAGTATAAACATCTGAAGGTTAGATCTAG-TATA
66 CAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCT-GCTATA
112312 TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATGC
1 TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATGC
* *
112377 CAAATCATCTTGGATCTACTTCAGTATAAACATCTGAAGGTTAGATCTGCTATC
66 CAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATA
*
112431 TTTGAGAACGTCTGAGAGTCAAATCTACTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATGC
1 TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATGC
* *
112496 CAAATCATCTTGGATTTGCTTCAGTATAAACATCTGAAGGTTAGAT-TGCTATC
66 CAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATA
112549 TTTGA
1 TTTGA
112554 TCTGTTCCTA
Statistics
Matches: 340, Mismatches: 19, Indels: 5
0.93 0.05 0.01
Matches are distributed among these distances:
118 13 0.04
119 326 0.96
120 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.34
Consensus pattern (119 bp):
TTTGAGAACGTCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATGC
CAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATA
Found at i:112668 original size:120 final size:125
Alignment explanation
Indices: 112535--112832 Score: 418
Period size: 127 Copynumber: 2.4 Consensus size: 125
112525 ACATCTGAAG
112535 GTTAGAT-TGCTATCTTTGATCTGTTCCTATAACAC-GGATG-CAAA-CATGCTATCTTC-ACTT
1 GTTAGATCTGCTATCTTTGATCTGTTCCTATAACACAGGATGCCAAATC-TG-T-TCTTCAACTT
112595 GTT-CCTATAAACACA-GATGCCATGCTGAAATCTT-ATCTGCTTCGCTGTAAGCACA-GAAT
63 GTTCCCTATAAACACAGGATGCCATGCTGAAATCTTAATCTGCTTCGCTGTAAGCACAGGAAT
*
112654 GTTAGATCTGCTATCTTTGATCTGTCCCTATAAACACAGGGATGCCAAATCTGTTCTTCAACTTG
1 GTTAGATCTGCTATCTTTGATCTGTTCCTAT-AACACA-GGATGCCAAATCTGTTCTTCAACTTG
112719 TTCCCTATAAACACAGGATGCCATGCTGAAATCTTCAATCTGCTTCGCTGTAAGCACAGGAAT
64 TTCCCTATAAACACAGGATGCCATGCTGAAATCTT-AATCTGCTTCGCTGTAAGCACAGGAAT
* * *
112782 GTCAGATCTACTATC-TTGATCTGTTCCCTATAAACATAGGATGCCAAATCT
1 GTTAGATCTGCTATCTTTGATCTGTT-CCTAT-AACACAGGATGCCAAATCT
112833 TGTTTCTTTG
Statistics
Matches: 161, Mismatches: 5, Indels: 18
0.88 0.03 0.10
Matches are distributed among these distances:
119 7 0.04
120 22 0.14
121 5 0.03
122 5 0.03
123 13 0.08
124 18 0.11
125 20 0.12
127 43 0.27
128 28 0.17
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (125 bp):
GTTAGATCTGCTATCTTTGATCTGTTCCTATAACACAGGATGCCAAATCTGTTCTTCAACTTGTT
CCCTATAAACACAGGATGCCATGCTGAAATCTTAATCTGCTTCGCTGTAAGCACAGGAAT
Found at i:113725 original size:21 final size:21
Alignment explanation
Indices: 113701--113741 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
113691 TCACCTTGGC
113701 CTCTCCATTTTTTTCTTTTTT
1 CTCTCCATTTTTTTCTTTTTT
**
113722 CTCTTTATTTTTTTCTTTTT
1 CTCTCCATTTTTTTCTTTTT
113742 CTTTTTCTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.05, C:0.20, G:0.00, T:0.76
Consensus pattern (21 bp):
CTCTCCATTTTTTTCTTTTTT
Found at i:113753 original size:21 final size:21
Alignment explanation
Indices: 113707--113759 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
113697 TGGCCTCTCC
113707 ATTTTTTTCTTTTTTCTCTTT
1 ATTTTTTTCTTTTTTCTCTTT
*
113728 ATTTTTTTC-TTTTTCTTTTT
1 ATTTTTTTCTTTTTTCTCTTT
*
113748 CTTTTTTT-TTTT
1 ATTTTTTTCTTTT
113760 GAAATAGAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 20 0.69
21 9 0.31
ACGTcount: A:0.04, C:0.11, G:0.00, T:0.85
Consensus pattern (21 bp):
ATTTTTTTCTTTTTTCTCTTT
Found at i:113759 original size:6 final size:6
Alignment explanation
Indices: 113710--113758 Score: 55
Period size: 6 Copynumber: 7.8 Consensus size: 6
113700 CCTCTCCATT
*
113710 TTTTTC TTTTTTC TCTTTATT TTTTTC TTTTTC TTTTTC TTTTT- TTTTT
1 TTTTTC -TTTTTC T-TTT-TC TTTTTC TTTTTC TTTTTC TTTTTC TTTTT
113759 TGAAATAGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
5 5 0.13
6 19 0.50
7 12 0.32
8 2 0.05
ACGTcount: A:0.02, C:0.12, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTTC
Found at i:113759 original size:12 final size:12
Alignment explanation
Indices: 113710--113759 Score: 64
Period size: 12 Copynumber: 3.9 Consensus size: 12
113700 CCTCTCCATT
113710 TTTTTCTTTTTTC
1 TTTTT-TTTTTTC
113723 TCTTTATTTTTTTC
1 T-TTT-TTTTTTTC
*
113737 TTTTTCTTTTTC
1 TTTTTTTTTTTC
113749 TTTTTTTTTTT
1 TTTTTTTTTTT
113760 GAAATAGAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
12 17 0.52
13 4 0.12
14 11 0.33
15 1 0.03
ACGTcount: A:0.02, C:0.12, G:0.00, T:0.86
Consensus pattern (12 bp):
TTTTTTTTTTTC
Found at i:122290 original size:27 final size:27
Alignment explanation
Indices: 122260--122437 Score: 214
Period size: 27 Copynumber: 6.6 Consensus size: 27
122250 ATATCGAGTC
* * * *
122260 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
*
122287 CGCACACTTAGTGCTACATAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
122314 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
122342 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
122369 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
122396 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
122423 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
122438 GTACAATTTA
Statistics
Matches: 132, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
27 108 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:122399 original size:82 final size:81
Alignment explanation
Indices: 122281--122436 Score: 242
Period size: 82 Copynumber: 1.9 Consensus size: 81
122271 TGCTATATAA
*
122281 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
122346 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
122363 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
122427 CACTTAGTGC
65 CACTTAGTGC
122437 TGTACAATTT
Statistics
Matches: 68, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
81 16 0.24
82 52 0.76
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Done.