Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003287.1 Hibiscus syriacus cultivar Beakdansim tig00006915_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: 59874
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Found at i:1745 original size:16 final size:17
Alignment explanation
Indices: 1717--1750 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
1707 GAAGTGGTTA
1717 AATAATAATGACGATTT
1 AATAATAATGACGATTT
1734 AATAAT-ATGACGATTT
1 AATAATAATGACGATTT
1750 A
1 A
1751 GAGAGTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.47, C:0.06, G:0.12, T:0.35
Consensus pattern (17 bp):
AATAATAATGACGATTT
Found at i:10070 original size:60 final size:60
Alignment explanation
Indices: 10006--10127 Score: 136
Period size: 60 Copynumber: 2.0 Consensus size: 60
9996 TCCCTCGATC
* * *
10006 ATAGGATATTGTTTTCTTCAGTCACCCGACTATTAAAAGTTACAAAATGATCATCCAACT
1 ATAGGACATTGTTTTCTTCAGTCACCCAACTATTAAAAGTTACAAAATGATCACCCAACT
* * * * **** *
10066 ATAGGGCGTTGTTTTGTTGAGTTTTTCAACTATTAAAAGTTACAAAATGATCACCCGACT
1 ATAGGACATTGTTTTCTTCAGTCACCCAACTATTAAAAGTTACAAAATGATCACCCAACT
10126 AT
1 AT
10128 TCATTATATT
Statistics
Matches: 50, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
60 50 1.00
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (60 bp):
ATAGGACATTGTTTTCTTCAGTCACCCAACTATTAAAAGTTACAAAATGATCACCCAACT
Found at i:10433 original size:27 final size:29
Alignment explanation
Indices: 10378--10432 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
10368 AAAACATCTT
*
10378 ATAGTCAGAGGATCATTTTGTAACTTTTA
1 ATAGTCAGAGGATCATTGTGTAACTTTTA
10407 ATAGTC-GAAGGATCATTGTGT-ACTTT
1 ATAGTCAG-AGGATCATTGTGTAACTTT
10433 ACCCTTAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 6 0.25
29 18 0.75
ACGTcount: A:0.29, C:0.11, G:0.20, T:0.40
Consensus pattern (29 bp):
ATAGTCAGAGGATCATTGTGTAACTTTTA
Found at i:10598 original size:39 final size:39
Alignment explanation
Indices: 10555--10646 Score: 103
Period size: 39 Copynumber: 2.4 Consensus size: 39
10545 GGACCTTTAG
** *
10555 ATGAGTGAAAATAATTTTACACATATGTAGGATTATTGA
1 ATGAGTGAAAATAATTTTACACATATGTAAAATCATTGA
* * * * *
10594 ATGAGTGAACATAGTTTTACATATATTTAAAATCGTTGA
1 ATGAGTGAAAATAATTTTACACATATGTAAAATCATTGA
*
10633 ATGAATGAAAATAA
1 ATGAGTGAAAATAA
10647 ATGAATTATA
Statistics
Matches: 42, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.43, C:0.05, G:0.16, T:0.35
Consensus pattern (39 bp):
ATGAGTGAAAATAATTTTACACATATGTAAAATCATTGA
Found at i:11170 original size:3 final size:3
Alignment explanation
Indices: 11164--11216 Score: 54
Period size: 3 Copynumber: 17.0 Consensus size: 3
11154 TTTACCCATT
* *
11164 TTA TTA TTTA TTTA TTG TTT TTA TTA TT- TTA TTTA TTA TTA TTA TTA
1 TTA TTA -TTA -TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
11211 TTA TTA
1 TTA TTA
11217 CAAATAGGCT
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
2 2 0.05
3 32 0.73
4 10 0.23
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (3 bp):
TTA
Found at i:11196 original size:21 final size:21
Alignment explanation
Indices: 11162--11212 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
11152 TTTTTACCCA
*
11162 TTTTATTA-TTTATTTATTGT
1 TTTTATTATTTTATTTATTAT
11182 TTTTATTATTTTATTTATTAT
1 TTTTATTATTTTATTTATTAT
*
11203 TATTATTATT
1 TTTTATTATT
11213 ATTACAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
20 8 0.29
21 20 0.71
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.75
Consensus pattern (21 bp):
TTTTATTATTTTATTTATTAT
Found at i:11216 original size:12 final size:13
Alignment explanation
Indices: 11164--11216 Score: 67
Period size: 12 Copynumber: 4.2 Consensus size: 13
11154 TTTACCCATT
11164 TTATTATTTATTTA
1 TTATTATTTA-TTA
*
11178 TTGTT-TTTATTA
1 TTATTATTTATTA
11190 TT-TTATTTATTA
1 TTATTATTTATTA
11202 TTATTA-TTATTA
1 TTATTATTTATTA
11214 TTA
1 TTA
11217 CAAATAGGCT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
11 2 0.06
12 23 0.64
13 7 0.19
14 4 0.11
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (13 bp):
TTATTATTTATTA
Found at i:12573 original size:19 final size:20
Alignment explanation
Indices: 12549--12599 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
12539 AATGACCAAT
12549 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATATAC
* *
12568 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATATAC
12588 AAAATCGCAACG
1 AAAATCGCAACG
12600 TTAAAAGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.43, C:0.24, G:0.18, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATATAC
Found at i:12593 original size:20 final size:20
Alignment explanation
Indices: 12549--12824 Score: 137
Period size: 20 Copynumber: 13.6 Consensus size: 20
12539 AATGACCAAT
* *
12549 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATTTAG
12568 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
** **
12588 AAAATCGCAACGTTA-AAAG
1 AAAATCGCAACGCGATTTAG
**
12607 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TTAG
* * **
12627 AAAATCGCAATGCGAGCTTCC
1 AAAATCGCAACGCGA-TTTAG
**
12648 AAGTTCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
* * *
12668 AAGAAATCGCAATGCGATTGAT
1 -A-AAATCGCAACGCGATTTAG
* * * *
12690 AGAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
* * *
12710 ATAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
* * *
12730 AGAGTCGCAACGCGATTGAG
1 AAAATCGCAACGCGATTTAG
* *
12750 AGAGTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* *
12773 AAAATCGCAACGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* * *
12793 AGAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
*
12813 AGAATCGCAACG
1 AAAATCGCAACG
12825 TTGAAAATAA
Statistics
Matches: 204, Mismatches: 41, Indels: 23
0.76 0.15 0.09
Matches are distributed among these distances:
19 31 0.15
20 128 0.63
21 15 0.07
22 14 0.07
23 16 0.08
ACGTcount: A:0.38, C:0.20, G:0.23, T:0.19
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:12725 original size:40 final size:40
Alignment explanation
Indices: 12652--12824 Score: 195
Period size: 40 Copynumber: 4.2 Consensus size: 40
12642 GCTTCCAAGT
*
12652 TCGCAACGCGATTTAGAAGAAATCGCAATGCGATTGATAGAA
1 TCGCAACGCGATTGAG-AG-AATCGCAATGCGATTGATAGAA
* * * * *
12694 TCGCAATGCGATTGATATAATCGCAATGCGATTGAGAGAG
1 TCGCAACGCGATTGAGAGAATCGCAATGCGATTGATAGAA
* *
12734 TCGCAACGCGATTGAGAGAGTCGCAACGCGATTTAGA-AGAAAA
1 TCGCAACGCGATTGAGAGAATCGCAATGCGA-TT-GATAG--AA
* *
12777 TCGCAACGCGACTGAGAGAATCGCAATGCGATTTATAGAA
1 TCGCAACGCGATTGAGAGAATCGCAATGCGATTGATAGAA
12817 TCGCAACG
1 TCGCAACG
12825 TTGAAAATAA
Statistics
Matches: 110, Mismatches: 16, Indels: 12
0.80 0.12 0.09
Matches are distributed among these distances:
40 56 0.51
41 6 0.05
42 19 0.17
43 29 0.26
ACGTcount: A:0.35, C:0.18, G:0.26, T:0.20
Consensus pattern (40 bp):
TCGCAACGCGATTGAGAGAATCGCAATGCGATTGATAGAA
Found at i:12942 original size:6 final size:6
Alignment explanation
Indices: 12931--12998 Score: 111
Period size: 6 Copynumber: 11.5 Consensus size: 6
12921 GACACGTATT
*
12931 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCCCG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
*
12979 ACCCCG ACCACG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACC
12999 CGAGACGAGA
Statistics
Matches: 60, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
5 5 0.08
6 55 0.92
ACGTcount: A:0.29, C:0.54, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:13697 original size:6 final size:6
Alignment explanation
Indices: 13686--13790 Score: 210
Period size: 6 Copynumber: 17.5 Consensus size: 6
13676 TCTCGTCTCG
13686 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
13734 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
13782 GGTCGT GGT
1 GGTCGT GGT
13791 AATACGTGTC
Statistics
Matches: 99, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 99 1.00
ACGTcount: A:0.00, C:0.16, G:0.50, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:13921 original size:20 final size:20
Alignment explanation
Indices: 13898--14152 Score: 138
Period size: 20 Copynumber: 12.6 Consensus size: 20
13888 TTATTTTCAA
13898 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
13918 CGTTGCGATTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* * * *
13938 CATTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
* * * *
13958 CATTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
* * *
13978 CATTGCGATTCTATAAATCG
1 CGTTGCGATTTTCTAAATCG
* * * * *
13998 CATTGCGATTCTATCAATCA
1 CGTTGCGATTTTCTAAATCG
*
14018 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
** ** *
14041 CGTTGCGAACTTGGAAGCTCG
1 CGTTGCGATTTTCTAA-ATCG
* *
14062 CGTTGCGATTTTCT--TTTG
1 CGTTGCGATTTTCTAAATCG
*** **
14080 ACCGTTGCGATTTTCTTTTTAA
1 --CGTTGCGATTTTCTAAATCG
14102 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
14122 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCTAAATCG
14141 CGTTGCGATTTT
1 CGTTGCGATTTT
14153 ATTGGTCATT
Statistics
Matches: 193, Mismatches: 34, Indels: 17
0.79 0.14 0.07
Matches are distributed among these distances:
18 2 0.01
19 17 0.09
20 144 0.75
21 13 0.07
22 4 0.02
23 13 0.07
ACGTcount: A:0.18, C:0.22, G:0.20, T:0.40
Consensus pattern (20 bp):
CGTTGCGATTTTCTAAATCG
Found at i:13944 original size:40 final size:40
Alignment explanation
Indices: 13900--14048 Score: 190
Period size: 40 Copynumber: 3.6 Consensus size: 40
13890 ATTTTCAACG
* *
13900 TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCA
1 TTGCGATTCTCTAAATCGCATTGCGATTCTCTCAATCGCA
* * *
13940 TTGCGATTCTCTCAGTCGCATTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTCTAAATCGCATTGCGATTCTCTCAATCGCA
* * *
13980 TTGCGATTCTATAAATCGCATTGCGATTCTATCAATCACA
1 TTGCGATTCTCTAAATCGCATTGCGATTCTCTCAATCGCA
*
14020 TTGCGATTTTCTTCTAAATCGCGTTGCGA
1 TTGCGA--TTC-TCTAAATCGCATTGCGA
14049 ACTTGGAAGC
Statistics
Matches: 93, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
40 75 0.81
42 3 0.03
43 15 0.16
ACGTcount: A:0.21, C:0.25, G:0.17, T:0.37
Consensus pattern (40 bp):
TTGCGATTCTCTAAATCGCATTGCGATTCTCTCAATCGCA
Found at i:13965 original size:60 final size:60
Alignment explanation
Indices: 13900--14048 Score: 190
Period size: 60 Copynumber: 2.4 Consensus size: 60
13890 ATTTTCAACG
* * * * *
13900 TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCATTGCGATTCTCTCAGTCGCA
1 TTGCGATTTTCTAAATCGCGTTGCGATTCTATAAATCGCATTGCGATTCTATCAATCACA
* * * *
13960 TTGCGATTCTCTCAGTCGCATTGCGATTCTATAAATCGCATTGCGATTCTATCAATCACA
1 TTGCGATTTTCTAAATCGCGTTGCGATTCTATAAATCGCATTGCGATTCTATCAATCACA
14020 TTGCGATTTTCTTCTAAATCGCGTTGCGA
1 TTGCGA--TT-TTCTAAATCGCGTTGCGA
14049 ACTTGGAAGC
Statistics
Matches: 73, Mismatches: 13, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
60 57 0.78
62 2 0.03
63 14 0.19
ACGTcount: A:0.21, C:0.25, G:0.17, T:0.37
Consensus pattern (60 bp):
TTGCGATTTTCTAAATCGCGTTGCGATTCTATAAATCGCATTGCGATTCTATCAATCACA
Found at i:14142 original size:19 final size:20
Alignment explanation
Indices: 14102--14152 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
14092 TTCTTTTTAA
*
14102 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCGAAATCG
*
14122 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCGAAATCG
14141 CGTTGCGATTTT
1 CGTTGCGATTTT
14153 ATTGGTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTTCGAAATCG
Found at i:18515 original size:15 final size:15
Alignment explanation
Indices: 18495--18526 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
18485 GATCAATACC
18495 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
18510 TTTTGCATACATTCA
1 TTTTGCATACATGCA
18525 TT
1 TT
18527 ATTCATTGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:21393 original size:21 final size:21
Alignment explanation
Indices: 21351--21393 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
21341 TTTCTGAGTT
* * *
21351 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
21372 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
21393 A
1 A
21394 CGAATATGAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:21454 original size:67 final size:67
Alignment explanation
Indices: 21351--21523 Score: 233
Period size: 67 Copynumber: 2.6 Consensus size: 67
21341 TTTCTGAGTT
* * *
21351 AGGGGAATCGGTACCCATTCAA-GGGGAACCGATACCCCCTCAACGAATATGAATTTCCAGAATA
1 AGGGGAATCGATACCC--CCAAGGGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATA
21415 CTAG
64 CTAG
* *
21419 AGGGGAATCGATACCCCCAAGGGGGAACCGATACCCCCTCAACGGATATGAAATTCCAGAATGCT
1 AGGGGAATCGATACCCCCAAGGGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATACT
21484 AG
66 AG
* * *
21486 AGGGGAACCGATA-CCCCAGGGGGGGAACCGATTCCCCC
1 AGGGGAATCGATACCCCCA-AGGGGGAACCGATACCCCC
21524 ATGAAAAAAA
Statistics
Matches: 95, Mismatches: 8, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
66 8 0.08
67 72 0.76
68 15 0.16
ACGTcount: A:0.31, C:0.28, G:0.26, T:0.15
Consensus pattern (67 bp):
AGGGGAATCGATACCCCCAAGGGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATACT
AG
Found at i:22197 original size:23 final size:23
Alignment explanation
Indices: 22130--22189 Score: 111
Period size: 23 Copynumber: 2.6 Consensus size: 23
22120 ATCATTATAT
*
22130 GGCACTACGGTGCAATTCTACGG
1 GGCACTTCGGTGCAATTCTACGG
22153 GGCACTTCGGTGCAATTCTACGG
1 GGCACTTCGGTGCAATTCTACGG
22176 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
22190 TTTATACGAG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.18, C:0.27, G:0.32, T:0.23
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGG
Found at i:28266 original size:21 final size:21
Alignment explanation
Indices: 28224--28266 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
28214 TTTCTGAGTT
* * *
28224 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
28245 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
28266 A
1 A
28267 CGAATATGAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:28324 original size:66 final size:66
Alignment explanation
Indices: 28246--28394 Score: 237
Period size: 66 Copynumber: 2.3 Consensus size: 66
28236 ACCCATTCAA
* *
28246 GGGGAACCGATACCCCCTCAACGAATATGAATTTCCAGAATACTAGA-GGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATACTAGAGGGGAACCGATA-CCCCA
28310 GG
65 GG
* *
28312 GGGGAACCGATACCCCCTCAACGGATATGAAATTCCAGAATGCTAGAGGGGAACCGATACCCCAG
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATACTAGAGGGGAACCGATACCCCAG
28377 G
66 G
*
28378 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
28395 ATGAAAAAAA
Statistics
Matches: 77, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
66 67 0.87
67 10 0.13
ACGTcount: A:0.31, C:0.29, G:0.26, T:0.15
Consensus pattern (66 bp):
GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATACTAGAGGGGAACCGATACCCCAG
G
Found at i:29071 original size:23 final size:23
Alignment explanation
Indices: 29005--29063 Score: 102
Period size: 22 Copynumber: 2.6 Consensus size: 23
28995 ATCATTATAT
*
29005 GGCACTACGGTGCAATTCTAC-G
1 GGCACTTCGGTGCAATTCTACGG
29027 GGCACTTCGGTGCAATTCTACGG
1 GGCACTTCGGTGCAATTCTACGG
29050 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
29064 TTTATACGAG
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
22 20 0.57
23 15 0.43
ACGTcount: A:0.19, C:0.27, G:0.31, T:0.24
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGG
Found at i:34858 original size:11 final size:10
Alignment explanation
Indices: 34842--34911 Score: 79
Period size: 11 Copynumber: 6.8 Consensus size: 10
34832 TATTATGCTT
*
34842 AAAAAATGAA
1 AAAAAAAGAA
34852 AAAAAAATGAA
1 AAAAAAA-GAA
34863 AAAAAAAGAAA
1 AAAAAAAG-AA
34874 AAAAAAAGAGA
1 AAAAAAAGA-A
* *
34885 AGAAGAAG-A
1 AAAAAAAGAA
34894 AAAAAAAGAA
1 AAAAAAAGAA
34904 AAAAAAAG
1 AAAAAAAG
34912 GGTCAAGATG
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
9 7 0.14
10 17 0.33
11 27 0.53
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:35798 original size:114 final size:114
Alignment explanation
Indices: 35597--35820 Score: 385
Period size: 114 Copynumber: 2.0 Consensus size: 114
35587 GTGCCACGTT
*
35597 CTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGATTTATCTGATCTG
1 CTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
* * *
35662 GTTTGGTATGAACCCCAAAACCAATCATTAGATTTAAAAGATGAATTTG
66 GTTCGGTAGGAACCCCAAAACCAATCATTAGAATTAAAAGATGAATTTG
35711 CTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 CTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
* * *
35776 GTTCGGTAGGAACCCCAGAACCAATCATTGGAATTGAAAGATGAA
66 GTTCGGTAGGAACCCCAAAACCAATCATTAGAATTAAAAGATGAA
35821 CTGTATGATC
Statistics
Matches: 103, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
114 103 1.00
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.30
Consensus pattern (114 bp):
CTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
GTTCGGTAGGAACCCCAAAACCAATCATTAGAATTAAAAGATGAATTTG
Found at i:36718 original size:113 final size:112
Alignment explanation
Indices: 36551--37310 Score: 847
Period size: 113 Copynumber: 6.7 Consensus size: 112
36541 TGCCAGTTAG
* * *
36551 AGTTCATAACGAGAAGAACCCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
* *
36616 AACTTTTTGTTTGAATTCATCATTCGATGGATCATCATTTCAAAAGAA
66 AACCTTTTGTTTGAATTCATCATTCGATGGATCAACATTTC-AAAGAA
* **
36664 AGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
* * * * * *
36729 AACCTTTTGTTTAAATTCATCATTTGATGGATCAACATTGCCAGGTAG
66 AACCTTTTGTTTGAATTCATCATTCGATGGATCAACATTTCAAAG-AA
36777 AGTTCATAATGAGAAGAACTCGTCATCTGAAGAA-GAAG-A-AA-TTCATAATGAGAAGAATTTG
1 AGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTG
* ** * * * *
36838 TTCAACCTTTTGCTCAAATCCATCACTTC-ATGGATCAGCTTTTCCAGAGAA
63 TTCAACCTTTTGTTTGAATTCATCA-TTCGATGGATCAACATTT-CAAAGAA
*
36889 ATTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
* * * * * *
36954 AACCTTTTGTTTGAATTCATCATTTGATGGATCAGCATTACCATGTAG
66 AACCTTTTGTTTGAATTCATCATTCGATGGATCAACATTTCAAAG-AA
* *
37002 AGTTCATAATGAGAAGAACTCGTCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
* * *
37067 AACTTTTTGTTTGAATTCATCATTCGATGGATCAACTTTTC-CAGAA
66 AACCTTTTGTTTGAATTCATCATTCGATGGATCAACATTTCAAAGAA
*
37113 AGTTCATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAGTTCATAATGAGAA-AATTTTGTT
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA-TTTGTT
* ** * *
37176 CAACCTTTT-TCTTG-ACTCTATCATAGAAGGAGATAGATCAACATCAACTTTTTCCAGAGAA
65 CAACCTTTTGT-TTGAATTC-ATCAT-----TCGATGGATC-A-A-C-A---TTT-CAAAGAA
* **
37237 AGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
*
37302 GACCTTTTG
66 AACCTTTTG
37311 CATGACTCTA
Statistics
Matches: 551, Mismatches: 64, Indels: 51
0.83 0.10 0.08
Matches are distributed among these distances:
109 18 0.03
110 51 0.09
111 29 0.05
112 78 0.14
113 274 0.50
114 1 0.00
115 12 0.02
116 12 0.02
117 1 0.00
118 1 0.00
122 3 0.01
123 1 0.00
124 32 0.06
125 37 0.07
126 1 0.00
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.30
Consensus pattern (112 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
AACCTTTTGTTTGAATTCATCATTCGATGGATCAACATTTCAAAGAA
Found at i:36904 original size:225 final size:224
Alignment explanation
Indices: 36512--37184 Score: 966
Period size: 225 Copynumber: 3.0 Consensus size: 224
36502 TTAGCAAAGA
* ** * * *
36512 TTTAAATCCATCATTCAATGGATCAACAGTGCCAGTTAGAGTTCATAACGAGAAGAAC-C--CAT
1 TTTAAATTCATCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCAT
*
36574 CTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTGAATTCATCAT
66 CTGAAGAA-GAAG-A-AA-TTCATAATGAGAAGAATTTGTTCAACTTTTTGTTTGAATTCATCAT
* * *
36639 TCGATGGATCATCATTTCAAAAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGA
127 TCGATGGATCAACTTTTC-CAAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGA
**
36704 AGTTCATAATGAGAAGAGCTTGTTCAACCTTTTG
191 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTG
36738 TTTAAATTCATCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCAT
1 TTTAAATTCATCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCAT
* * ** *
36803 CTGAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTC-
66 CTGAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACTTTTTGTTTGAATTCATCA-TTCG
* * *
36867 ATGGATCAGCTTTTCCAGAGAAATTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
130 ATGGATCAACTTTTCCA-AGAAAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGT
36932 TCATAATGAGAAGAATTTGTTCAACCTTTTG
194 TCATAATGAGAAGAATTTGTTCAACCTTTTG
* * * *
36963 TTTGAATTCATCATTTGATGGATCAGCATTACCATGTAGAGTTCATAATGAGAAGAACTCGTC-T
1 TTTAAATTCATCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCAT
**
37027 GAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACTTTTTGTTTGAATTCATCATTC
66 -CTGAA-GAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACTTTTTGTTTGAATTCATCATTC
37092 GATGGATCAACTTTTCC-AGAAAGTTCATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAGT
129 GATGGATCAACTTTTCCAAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGT
37155 TCATAATGAGAA-AATTTTGTTCAACCTTTT
194 TCATAATGAGAAGAA-TTTGTTCAACCTTTT
37185 TCTTGACTCT
Statistics
Matches: 405, Mismatches: 33, Indels: 21
0.88 0.07 0.05
Matches are distributed among these distances:
222 2 0.00
223 40 0.10
224 33 0.08
225 191 0.47
226 122 0.30
227 2 0.00
228 4 0.01
229 11 0.03
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (224 bp):
TTTAAATTCATCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCAT
CTGAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACTTTTTGTTTGAATTCATCATTCGA
TGGATCAACTTTTCCAAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTC
ATAATGAGAAGAATTTGTTCAACCTTTTG
Found at i:37322 original size:125 final size:123
Alignment explanation
Indices: 37097--37454 Score: 446
Period size: 125 Copynumber: 2.9 Consensus size: 123
37087 CATTCGATGG
* *
37097 ATCAACTTTTCC--AGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATA
1 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATA
* ** * * *
37160 ATGAGAAAATTTTGTTCAACCTTTTTCTTGACTCTATCATAGAAGGAGATAGATCAAC
66 ATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAAC
37218 ATCAACTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCA
1 ATCAAC-TTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG-AAGAAGAAGAAGTTCA
* * * *
37283 TAATGAGAAGAGCTTGTTCGACCTTTTGCATGACTCTATCACAGAATGAGATATATCATC
64 TAATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAAC
* * * * *
37343 ATCAGCATTTCCAGA-AGGAGTTCACAATGAGAAGAACTCATCT---GAAGAAGAAGAAGTTCAC
1 ATCAACTTTTCCAGAGA-AAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCAT
*
37404 AATGAGAAGAGCTTGTTCAACC-TTTGC-TAGATTAC-ATCACAGAAGGAGATA
65 AATGAGAAGAGCTTGTTCAACCTTTTGCAT-GACT-CTATCACAGAAGGAGATA
37455 AATTGTCATC
Statistics
Matches: 210, Mismatches: 20, Indels: 16
0.85 0.08 0.07
Matches are distributed among these distances:
118 1 0.00
119 23 0.11
120 38 0.18
121 7 0.03
122 6 0.03
123 1 0.00
124 64 0.30
125 70 0.33
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.27
Consensus pattern (123 bp):
ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATA
ATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAAC
Found at i:37413 original size:17 final size:17
Alignment explanation
Indices: 37355--37413 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
37345 CAGCATTTCC
*
37355 AGAAGGAGTTCACAATG
1 AGAAGAAGTTCACAATG
*
37372 AGAAGAA-CTCATCTGAA-G
1 AGAAGAAGTTCA-C--AATG
37390 AAGAAGAAGTTCACAATG
1 -AGAAGAAGTTCACAATG
37408 AGAAGA
1 AGAAGA
37414 GCTTGTTCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 12
0.69 0.06 0.25
Matches are distributed among these distances:
16 3 0.09
17 15 0.45
18 2 0.06
19 10 0.30
20 3 0.09
ACGTcount: A:0.47, C:0.12, G:0.25, T:0.15
Consensus pattern (17 bp):
AGAAGAAGTTCACAATG
Found at i:37674 original size:3 final size:3
Alignment explanation
Indices: 37660--37706 Score: 78
Period size: 3 Copynumber: 16.0 Consensus size: 3
37650 ATTTATTTAT
*
37660 TTA TTG TTA TTA TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
37707 CAAACATGCT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
2 2 0.05
3 39 0.95
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:37677 original size:20 final size:20
Alignment explanation
Indices: 37655--37706 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 20
37645 ATTTTATTTA
*
37655 TTTATTTATTGTTATTATTAT
1 TTTA-TTATTATTATTATTAT
37676 TTTATTATTATTATTATTAT
1 TTTATTATTATTATTATTAT
37696 TATTATTATTA
1 T-TTATTATTA
37707 CAAACATGCT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 16 0.55
21 13 0.45
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (20 bp):
TTTATTATTATTATTATTAT
Found at i:39254 original size:20 final size:19
Alignment explanation
Indices: 39229--39270 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
39219 TTATTTTATA
39229 AATTATATATTAATTGTTTT
1 AATTATATATTAATT-TTTT
* *
39249 AATTATTTATTTATTTTTT
1 AATTATATATTAATTTTTT
39268 AAT
1 AAT
39271 ATCAAAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
AATTATATATTAATTTTTT
Found at i:41190 original size:17 final size:17
Alignment explanation
Indices: 41149--41192 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
41139 AATTTCCTCG
41149 AGTTTTTAAATAAAATA
1 AGTTTTTAAATAAAATA
* * *
41166 AATATTTAATTAAAATA
1 AGTTTTTAAATAAAATA
*
41183 TGTTTTTAAA
1 AGTTTTTAAA
41193 CATATCCTTG
Statistics
Matches: 20, Mismatches: 7, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (17 bp):
AGTTTTTAAATAAAATA
Found at i:48820 original size:48 final size:48
Alignment explanation
Indices: 48768--48899 Score: 151
Period size: 48 Copynumber: 2.8 Consensus size: 48
48758 AATATTTTAC
* *
48768 CTGATTTTTGATTTGATTTCTGATCTGATACTTGACATGGATTCTGAT
1 CTGATTTTTGAATTGATTTCTGATATGATACTTGACATGGATTCTGAT
* * * *
48816 CTGATATCTGACATGGA-TTCTGATATGATACTTGACTTGGATTCTGAT
1 CTGATTTTTGA-ATTGATTTCTGATATGATACTTGACATGGATTCTGAT
* **
48864 CTG-TTACTTGACCTGATTTCTGATATGATACTTGAC
1 CTGATT-TTTGAATTGATTTCTGATATGATACTTGAC
48900 CTGATTTATG
Statistics
Matches: 69, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
47 3 0.04
48 63 0.91
49 3 0.04
ACGTcount: A:0.23, C:0.15, G:0.19, T:0.43
Consensus pattern (48 bp):
CTGATTTTTGAATTGATTTCTGATATGATACTTGACATGGATTCTGAT
Found at i:48837 original size:12 final size:12
Alignment explanation
Indices: 48800--48862 Score: 51
Period size: 12 Copynumber: 5.2 Consensus size: 12
48790 ATCTGATACT
48800 TGACATGGATTC
1 TGACATGGATTC
48812 TGATC-T-GATATC
1 TGA-CATGGAT-TC
48824 TGACATGGATTC
1 TGACATGGATTC
* *
48836 TGATAT-GATAC
1 TGACATGGATTC
*
48847 TTGACTTGGATTC
1 -TGACATGGATTC
48860 TGA
1 TGA
48863 TCTGTTACTT
Statistics
Matches: 40, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
11 8 0.20
12 24 0.60
13 8 0.20
ACGTcount: A:0.25, C:0.14, G:0.22, T:0.38
Consensus pattern (12 bp):
TGACATGGATTC
Found at i:48906 original size:24 final size:24
Alignment explanation
Indices: 48785--48899 Score: 153
Period size: 24 Copynumber: 4.8 Consensus size: 24
48775 TTGATTTGAT
48785 TTCTGATCTGATACTTGACATGGA
1 TTCTGATCTGATACTTGACATGGA
48809 TTCTGATCTGATA-TCTGACATGGA
1 TTCTGATCTGATACT-TGACATGGA
* *
48833 TTCTGATATGATACTTGACTTGGA
1 TTCTGATCTGATACTTGACATGGA
* *
48857 TTCTGATCTGTTACTTGACCT-GA
1 TTCTGATCTGATACTTGACATGGA
*
48880 TTTCTGATATGATACTTGAC
1 -TTCTGATCTGATACTTGAC
48900 CTGATTTATG
Statistics
Matches: 81, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
23 3 0.04
24 77 0.95
25 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.41
Consensus pattern (24 bp):
TTCTGATCTGATACTTGACATGGA
Found at i:48922 original size:24 final size:24
Alignment explanation
Indices: 48836--48909 Score: 87
Period size: 24 Copynumber: 3.1 Consensus size: 24
48826 ACATGGATTC
* *
48836 TGATATGATACTTGACTTGGA-TTC
1 TGATATGATACTTGACCT-GATTTA
* * *
48860 TGATCTGTTACTTGACCTGATTTC
1 TGATATGATACTTGACCTGATTTA
48884 TGATATGATACTTGACCTGATTTA
1 TGATATGATACTTGACCTGATTTA
48908 TG
1 TG
48910 TTTTGATTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
23 2 0.05
24 41 0.95
ACGTcount: A:0.23, C:0.15, G:0.19, T:0.43
Consensus pattern (24 bp):
TGATATGATACTTGACCTGATTTA
Found at i:50348 original size:23 final size:21
Alignment explanation
Indices: 50321--50371 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 21
50311 AATAATAATG
* *
50321 TAAATTAAAGTATATTTAATCAA
1 TAAATTAAAATAAATTT-AT-AA
*
50344 TAAATCAAAATAAATTTATAA
1 TAAATTAAAATAAATTTATAA
50365 TAAATTA
1 TAAATTA
50372 TATATTTTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 8 0.33
22 2 0.08
23 14 0.58
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (21 bp):
TAAATTAAAATAAATTTATAA
Found at i:50578 original size:17 final size:17
Alignment explanation
Indices: 50556--50592 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
50546 ACGTGTATAC
* *
50556 TTAATTTTTATTCATCT
1 TTAATTTATATTAATCT
50573 TTAATTTATATTAATCT
1 TTAATTTATATTAATCT
50590 TTA
1 TTA
50593 TATGATAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.30, C:0.08, G:0.00, T:0.62
Consensus pattern (17 bp):
TTAATTTATATTAATCT
Found at i:50608 original size:27 final size:27
Alignment explanation
Indices: 50578--50633 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
50568 CATCTTTAAT
** *
50578 TTATATTAATCTTTATATGATAATAAA
1 TTATATTAAAATTTATATAATAATAAA
* *
50605 TTATTTTAAAATTTATATAATAATTAA
1 TTATATTAAAATTTATATAATAATAAA
50632 TT
1 TT
50634 TTAATGTATT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (27 bp):
TTATATTAAAATTTATATAATAATAAA
Found at i:50847 original size:60 final size:60
Alignment explanation
Indices: 50754--50908 Score: 238
Period size: 60 Copynumber: 2.6 Consensus size: 60
50744 GTACTCAAAG
* * * *
50754 TATGACTCTTATTTTAAATTAGTCTCTAAAATTTTAAATATATTAATTTTATTCTTAAAC
1 TATGACTATCATTTTAAATTAGTCTCTAAAATTTTAAATATATTAATTGTATTCCTAAAC
*
50814 TATGACTATCATTCTAAATTAGTCTCTAAAATTTTAAATATATTAATTGTATTCCTAAAC
1 TATGACTATCATTTTAAATTAGTCTCTAAAATTTTAAATATATTAATTGTATTCCTAAAC
* * *
50874 AATGACTATCATTTTAAATTAGTCTTTAAACTTTT
1 TATGACTATCATTTTAAATTAGTCTCTAAAATTTT
50909 GAACATTTCA
Statistics
Matches: 86, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 86 1.00
ACGTcount: A:0.37, C:0.12, G:0.05, T:0.47
Consensus pattern (60 bp):
TATGACTATCATTTTAAATTAGTCTCTAAAATTTTAAATATATTAATTGTATTCCTAAAC
Found at i:50931 original size:60 final size:60
Alignment explanation
Indices: 50754--50995 Score: 217
Period size: 60 Copynumber: 4.0 Consensus size: 60
50744 GTACTCAAAG
* * * * * * *
50754 TATGACTCTTATTTTAAATTAGTCTCTAAAATTTTAAATATATTAATTTTATTCTTAAAC
1 TATGACTATCATTCTAAATTAGTCTCTAAAATTTTAAACATATTAATTTCATCCCTAAAC
* *
50814 TATGACTATCATTCTAAATTAGTCTCTAAAATTTTAAATATATTAATTGT-ATTCCTAAAC
1 TATGACTATCATTCTAAATTAGTCTCTAAAATTTTAAACATATTAATT-TCATCCCTAAAC
* * * * * *
50874 AATGACTATCATTTTAAATTAGTCTTTAAACTTTTGAACAT-TTCAATTTCATCCCTAACC
1 TATGACTATCATTCTAAATTAGTCTCTAAAATTTTAAACATATT-AATTTCATCCCTAAAC
* * * * *
50934 TATGA-AATTCATTCTAAATTGGTC-CCAAACTTTTTGAACAT-TCTAATTTCATCCC-AAAC
1 TATGACTA-TCATTCTAAATTAGTCTCTAAA-ATTTTAAACATAT-TAATTTCATCCCTAAAC
50993 TAT
1 TAT
50996 ATGTATATTC
Statistics
Matches: 156, Mismatches: 20, Indels: 13
0.83 0.11 0.07
Matches are distributed among these distances:
59 13 0.08
60 141 0.90
61 2 0.01
ACGTcount: A:0.36, C:0.16, G:0.05, T:0.43
Consensus pattern (60 bp):
TATGACTATCATTCTAAATTAGTCTCTAAAATTTTAAACATATTAATTTCATCCCTAAAC
Found at i:51188 original size:60 final size:60
Alignment explanation
Indices: 51111--51271 Score: 191
Period size: 60 Copynumber: 2.7 Consensus size: 60
51101 AATGAATTTG
* * * ** *
51111 GGGATGGAATTAGAATATTCAAAAGTTT-GGAGACCAATTTAGAAAGAGTTTCATATTTTA
1 GGGATGAAATTAAAATATTCAAAAGTTTAAG-GACCAATTTAGAAAGAGAGTCATAGTTTA
* * *
51171 GGGATGAAATTAAAATATTAAAAAGTTTAAGGACTAATTTAGAACGAGAGTCATAGTTTA
1 GGGATGAAATTAAAATATTCAAAAGTTTAAGGACCAATTTAGAAAGAGAGTCATAGTTTA
* *
51231 GGGATGGAAA-TGAAATATTCAAAAGTTTAAGGATCAATTTA
1 GGGAT-GAAATTAAAATATTCAAAAGTTTAAGGACCAATTTA
51272 AAATAAGGGT
Statistics
Matches: 86, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
60 81 0.94
61 5 0.06
ACGTcount: A:0.42, C:0.06, G:0.21, T:0.31
Consensus pattern (60 bp):
GGGATGAAATTAAAATATTCAAAAGTTTAAGGACCAATTTAGAAAGAGAGTCATAGTTTA
Found at i:51291 original size:60 final size:60
Alignment explanation
Indices: 51105--51294 Score: 156
Period size: 60 Copynumber: 3.2 Consensus size: 60
51095 TATTTGAATG
* * * * * * *
51105 AATTTGGGGATGGAATTAGAATATTCAAAAGTTT-GGAGACCAATTT-AGA-AAGAGTTTCAT
1 AATTTAGGGATGAAATTAAAATATTAAAAAGTTTAAG-GACTAATTTAAAACAAGAG--TCAT
* * *
51165 ATTTTAGGGATGAAATTAAAATATTAAAAAGTTTAAGGACTAATTTAGAACGAGAGTCAT
1 AATTTAGGGATGAAATTAAAATATTAAAAAGTTTAAGGACTAATTTAAAACAAGAGTCAT
* * * * * *
51225 AGTTTAGGGATGGAAA-TGAAATATTCAAAAGTTTAAGGA-TCAATTTAAAATAAGGGTTAT
1 AATTTAGGGAT-GAAATTAAAATATTAAAAAGTTTAAGGACT-AATTTAAAACAAGAGTCAT
51285 AATTTAGGGA
1 AATTTAGGGA
51295 CATCTGATGC
Statistics
Matches: 106, Mismatches: 19, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
59 1 0.01
60 95 0.90
61 6 0.06
62 4 0.04
ACGTcount: A:0.42, C:0.05, G:0.22, T:0.32
Consensus pattern (60 bp):
AATTTAGGGATGAAATTAAAATATTAAAAAGTTTAAGGACTAATTTAAAACAAGAGTCAT
Found at i:53265 original size:21 final size:21
Alignment explanation
Indices: 53223--53266 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
53213 GGTAAAAAAA
* *
53223 TTACCTAAAATATTATTATTT
1 TTACCTAAAACATTAATATTT
*
53244 TTACCTAAAACATTAATGTTT
1 TTACCTAAAACATTAATATTT
53265 TT
1 TT
53267 TAATATTTTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.11, G:0.02, T:0.50
Consensus pattern (21 bp):
TTACCTAAAACATTAATATTT
Found at i:53306 original size:27 final size:27
Alignment explanation
Indices: 53276--53334 Score: 91
Period size: 27 Copynumber: 2.2 Consensus size: 27
53266 TTAATATTTT
* *
53276 CGGTAAAGTGTCCAACAATAACAAAAC
1 CGGTAAAGCGCCCAACAATAACAAAAC
*
53303 CGGTAAAGCGCCCAATAATAACAAAAC
1 CGGTAAAGCGCCCAACAATAACAAAAC
53330 CGGTA
1 CGGTA
53335 GAAATAATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.46, C:0.24, G:0.17, T:0.14
Consensus pattern (27 bp):
CGGTAAAGCGCCCAACAATAACAAAAC
Found at i:54124 original size:18 final size:18
Alignment explanation
Indices: 54101--54137 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
54091 TTAAACAATG
54101 TGAGCTTCTCAAATCCTA
1 TGAGCTTCTCAAATCCTA
54119 TGAGCTTCTCAAATCCTA
1 TGAGCTTCTCAAATCCTA
54137 T
1 T
54138 ATTGTTCGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.11, T:0.35
Consensus pattern (18 bp):
TGAGCTTCTCAAATCCTA
Found at i:56081 original size:50 final size:50
Alignment explanation
Indices: 56001--56101 Score: 184
Period size: 50 Copynumber: 2.0 Consensus size: 50
55991 CAAGTTCAAA
56001 ATCTCTCATTAGATGCATGAACTTGTAACAAAAGTAAACATTTATGTAAT
1 ATCTCTCATTAGATGCATGAACTTGTAACAAAAGTAAACATTTATGTAAT
* *
56051 ATCTGTCATTAGATGCTTGAACTTGTAACAAAAGTAAACATTTATGTAAT
1 ATCTCTCATTAGATGCATGAACTTGTAACAAAAGTAAACATTTATGTAAT
56101 A
1 A
56102 AAACTCTGGT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (50 bp):
ATCTCTCATTAGATGCATGAACTTGTAACAAAAGTAAACATTTATGTAAT
Found at i:58355 original size:30 final size:30
Alignment explanation
Indices: 58300--58366 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
58290 GTGCCTGAGA
*
58300 AGCAGCACCAGGATTATTAAAGAGTG-CTTG
1 AGCAGCACCAGGATTATGAAAGAGTGTC-TG
* * *
58330 AGCAGCACCAGGGTTATGGAGGAGTGTCTG
1 AGCAGCACCAGGATTATGAAAGAGTGTCTG
58360 AGCAGCA
1 AGCAGCA
58367 GCCGTGGGAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 31 0.97
31 1 0.03
ACGTcount: A:0.30, C:0.18, G:0.33, T:0.19
Consensus pattern (30 bp):
AGCAGCACCAGGATTATGAAAGAGTGTCTG
Done.