Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003994.1 Hibiscus syriacus cultivar Beakdansim tig00008699_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: 111005
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:569 original size:21 final size:22
Alignment explanation
Indices: 522--571 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
512 TTCTCTGTTT
*
522 TTTTTTTCTGTCTTCCTTCTTC
1 TTTTTTTCTGTCTCCCTTCTTC
*
544 GTTTTTTCTGTCTCCCTTC-TC
1 TTTTTTTCTGTCTCCCTTCTTC
565 TTTTTTT
1 TTTTTTT
572 TTTTTTTCAG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 8 0.32
22 17 0.68
ACGTcount: A:0.00, C:0.26, G:0.06, T:0.68
Consensus pattern (22 bp):
TTTTTTTCTGTCTCCCTTCTTC
Found at i:576 original size:26 final size:25
Alignment explanation
Indices: 512--575 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 25
502 GTTTTTCCTT
*
512 TTCTCTGTTTTTTTTTTCTGTCTTCC
1 TTCTCT-TTTTTTTTTTCTGTCTCCC
**
538 -T-TC-TTCGTTTTTTCTGTCTCCC
1 TTCTCTTTTTTTTTTTCTGTCTCCC
560 TTCTCTTTTTTTTTTT
1 TTCTCTTTTTTTTTTT
576 TTTCAGGTTC
Statistics
Matches: 30, Mismatches: 5, Indels: 7
0.71 0.12 0.17
Matches are distributed among these distances:
22 16 0.53
23 1 0.03
24 4 0.13
25 9 0.30
ACGTcount: A:0.00, C:0.23, G:0.06, T:0.70
Consensus pattern (25 bp):
TTCTCTTTTTTTTTTTCTGTCTCCC
Found at i:1042 original size:3 final size:3
Alignment explanation
Indices: 1034--1151 Score: 191
Period size: 3 Copynumber: 38.7 Consensus size: 3
1024 TATATATATT
* *
1034 TAA TAA TAA TAA TAA TAA TGA TGA TAA TAA TATA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA
*
1080 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAG TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1128 TAA TAA TATA TAA TAA TAA TAA TA
1 TAA TAA TA-A TAA TAA TAA TAA TA
1152 TGGATAAAAA
Statistics
Matches: 109, Mismatches: 4, Indels: 4
0.93 0.03 0.03
Matches are distributed among these distances:
3 103 0.94
4 6 0.06
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1803 original size:112 final size:113
Alignment explanation
Indices: 1463--2101 Score: 1064
Period size: 112 Copynumber: 5.7 Consensus size: 113
1453 AGAATTATGC
* *
1463 AAAA-GTTGAACAAGTTCTTCT-A-TATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * * * *
1525 TATGAAC-TTCTCCGG-AAAGATAATCCATCAATTGATGAATTCAGGT
66 TATGAACTTTCTCTGGAAAAGTTGATCCCTCAAATGATGGATTCAGGT
* *
1571 AAAAGGTTGAACAAATTCTTCTAATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
1636 TATGAACTTTCTCTGGAAAAGATGATCCCTCAAATGATGGATTCAGGT
66 TATGAACTTTCTCTGGAAAAGTTGATCCCTCAAATGATGGATTCAGGT
*
1684 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG-TCTTCTTAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
1748 TATGAACTTTTTCTGGAAAAGTTGATCCCTCAAATGATGGATTCAGGT
66 TATGAACTTTCTCTGGAAAAGTTGATCCCTCAAATGATGGATTCAGGT
*
1796 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTT-TTAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1860 TATGAACTTTCTCTGGAAAAGTTGATCCCTCAAATGATGGATTCAGGT
66 TATGAACTTTCTCTGGAAAAGTTGATCCCTCAAATGATGGATTCAGGT
1908 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTT-TTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
1972 TATGAACTTTCTCTGGAAAAGTTGATCCATCAAATGATGGATTCAGGT
66 TATGAACTTTCTCTGGAAAAGTTGATCCCTCAAATGATGGATTCAGGT
2020 AAAAGGTTGAACAAATTC-T-TCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
2083 TATGAACTCTCTCTGGAAA
66 TATGAACTTTCTCTGGAAA
2102 GCTAATCTTT
Statistics
Matches: 506, Mismatches: 17, Indels: 13
0.94 0.03 0.02
Matches are distributed among these distances:
108 4 0.01
109 16 0.03
110 24 0.05
111 99 0.20
112 279 0.55
113 84 0.17
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (113 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTTTCTCTGGAAAAGTTGATCCCTCAAATGATGGATTCAGGT
Found at i:3278 original size:82 final size:83
Alignment explanation
Indices: 2953--3407 Score: 753
Period size: 82 Copynumber: 5.6 Consensus size: 83
2943 CATACCAAAC
2953 CAGATAACTCAAAGAACACTTCCAG-A-ATGCTATTGGCAAATTCATCTTCTAAACTCAATGCTT
1 CAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATGCTT
3016 GATTCTGTCCAATCAGAT
66 GATTCTGTCCAATCAGAT
* *
3034 CAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAATTCAATGCTT
1 CAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATGCTT
3099 GATTCTGTCCAATCAGAT
66 GATTCTGTCCAATCAGAT
** *
3117 CAGATAACTCAAAGAACACTT-C-GAAGATGCTATTGGTGAATTCATCTTCTAAACTCAATGATT
1 CAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATGCTT
*
3180 G-TTCTGTCCAACCAGAT
66 GATTCTGTCCAATCAGAT
*
3197 CAGATATCTCAAAGAACACTTCCAGAAGATGCTATTGGC-AATTCATCTTCTAAACTCAATGCTT
1 CAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATGCTT
*
3261 GATTCTGTCTAATCAGAT
66 GATTCTGTCCAATCAGAT
* * *
3279 CAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAATTC-ATGATT
1 CAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATGCTT
*
3343 GATTCTGTCCAACCAGAT
66 GATTCTGTCCAATCAGAT
3361 CAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCAT
1 CAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCAT
3408 TTGTTCTATT
Statistics
Matches: 349, Mismatches: 19, Indels: 11
0.92 0.05 0.03
Matches are distributed among these distances:
80 35 0.10
81 88 0.25
82 136 0.39
83 90 0.26
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.29
Consensus pattern (83 bp):
CAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATGCTT
GATTCTGTCCAATCAGAT
Found at i:4531 original size:1 final size:1
Alignment explanation
Indices: 4527--4588 Score: 79
Period size: 1 Copynumber: 62.0 Consensus size: 1
4517 CTTGACCCCC
* * * * *
4527 TTTTTTTCTTCTTCTTTTTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
4589 CTTTCTTTTC
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
1 51 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (1 bp):
T
Found at i:4545 original size:14 final size:13
Alignment explanation
Indices: 4526--4600 Score: 86
Period size: 14 Copynumber: 5.8 Consensus size: 13
4516 CCTTGACCCC
4526 CTTTTTTTCTTCTT
1 CTTTTTTTCTT-TT
4540 CTTTTTTTCTTTT
1 CTTTTTTTCTTTT
4553 -TTTTTTT-TTTT
1 CTTTTTTTCTTTT
4564 -TTTTTTT-TTTT
1 CTTTTTTTCTTTT
*
4575 TTTTTTTTCTTTTT
1 CTTTTTTTC-TTTT
4589 CTTTCTTTTCTT
1 CTTT-TTTTCTT
4601 CAAGCATAAT
Statistics
Matches: 56, Mismatches: 1, Indels: 8
0.86 0.02 0.12
Matches are distributed among these distances:
11 15 0.27
12 14 0.25
13 2 0.04
14 20 0.36
15 5 0.09
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (13 bp):
CTTTTTTTCTTTT
Found at i:8132 original size:17 final size:19
Alignment explanation
Indices: 8107--8142 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
8097 ATTTATGAAA
8107 TAAATAAATGTAAA-AATG
1 TAAATAAATGTAAAGAATG
8125 TAAA-AAATGTAAAGAATG
1 TAAATAAATGTAAAGAATG
8143 ATTGCCATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.61, C:0.00, G:0.14, T:0.25
Consensus pattern (19 bp):
TAAATAAATGTAAAGAATG
Found at i:15170 original size:13 final size:15
Alignment explanation
Indices: 15148--15184 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
15138 TCTGACAGAA
15148 AAAT-AAATAC-TG-
1 AAATAAAATACTTGC
15160 AAATAAAATACTTGC
1 AAATAAAATACTTGC
15175 AAATAAAATA
1 AAATAAAATA
15185 AAACATATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.18
13 6 0.27
14 2 0.09
15 10 0.45
ACGTcount: A:0.62, C:0.08, G:0.05, T:0.24
Consensus pattern (15 bp):
AAATAAAATACTTGC
Found at i:15256 original size:26 final size:26
Alignment explanation
Indices: 15192--15256 Score: 60
Period size: 26 Copynumber: 2.5 Consensus size: 26
15182 ATAAAACATA
* *
15192 TAAATATTATAAAAATAAAAAATAAAT
1 TAAATA-TATGAAAAGAAAAAATAAAT
* * *
15219 AAAAAATTTGAAAAGAAAGAAA-AAAT
1 TAAATATATGAAAAGAAA-AAATAAAT
15245 TAAATATATGAA
1 TAAATATATGAA
15257 CTTTTAATTT
Statistics
Matches: 29, Mismatches: 8, Indels: 3
0.73 0.20 0.08
Matches are distributed among these distances:
26 22 0.76
27 7 0.24
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.25
Consensus pattern (26 bp):
TAAATATATGAAAAGAAAAAATAAAT
Found at i:15914 original size:14 final size:16
Alignment explanation
Indices: 15895--15927 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
15885 AAAATAAATA
15895 TTAAAAT-AA-TTTAT
1 TTAAAATAAATTTTAT
15909 TTAAAATAAATTTTAT
1 TTAAAATAAATTTTAT
15925 TTA
1 TTA
15928 TATAACAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.41
15 2 0.12
16 8 0.47
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTAAAATAAATTTTAT
Found at i:16865 original size:19 final size:18
Alignment explanation
Indices: 16841--16908 Score: 64
Period size: 19 Copynumber: 3.4 Consensus size: 18
16831 GGTTTAGTAG
16841 TTTTTTTTCCTTTCTCTGT
1 TTTTTTTTCCTTTCTCT-T
*
16860 TTTTTTTTCTGTCTTCCTTCTT
1 TTTTTTTTC---CTTTC-TCTT
*
16882 TTTTTTTCTCCCTTCTCTT
1 TTTTTTT-TCCTTTCTCTT
16901 TTTTTTTT
1 TTTTTTTT
16909 TCAGGTTCGG
Statistics
Matches: 41, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
18 1 0.02
19 20 0.49
20 3 0.07
22 12 0.29
23 5 0.12
ACGTcount: A:0.00, C:0.22, G:0.03, T:0.75
Consensus pattern (18 bp):
TTTTTTTTCCTTTCTCTT
Found at i:16895 original size:17 final size:17
Alignment explanation
Indices: 16861--16906 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 17
16851 TTTCTCTGTT
*
16861 TTTTTTTCTGTCTTCCTTC
1 TTTTTTT-T-TCTCCCTTC
16880 TTTTTTTTTCTCCCTTC
1 TTTTTTTTTCTCCCTTC
16897 TCTTTTTTTT
1 T-TTTTTTTT
16907 TTTCAGGTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 9 0.36
18 9 0.36
19 7 0.28
ACGTcount: A:0.00, C:0.24, G:0.02, T:0.74
Consensus pattern (17 bp):
TTTTTTTTTCTCCCTTC
Found at i:16910 original size:21 final size:21
Alignment explanation
Indices: 16841--16910 Score: 81
Period size: 21 Copynumber: 3.4 Consensus size: 21
16831 GGTTTAGTAG
* *
16841 TTTTTTT-TCCTTTCTCTGTT
1 TTTTTTTCTCCCTTCTCTTTT
**
16861 TTTTTTTCTGTCTTC-CTTCTT
1 TTTTTTTCTCCCTTCTCTT-TT
16882 TTTTTTTCTCCCTTCTCTTTT
1 TTTTTTTCTCCCTTCTCTTTT
16903 TTTTTTTC
1 TTTTTTTC
16911 AGGTTCGGGT
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
20 9 0.22
21 29 0.71
22 3 0.07
ACGTcount: A:0.00, C:0.23, G:0.03, T:0.74
Consensus pattern (21 bp):
TTTTTTTCTCCCTTCTCTTTT
Found at i:17382 original size:3 final size:3
Alignment explanation
Indices: 17374--17468 Score: 154
Period size: 3 Copynumber: 31.7 Consensus size: 3
17364 TTAATATATT
*
17374 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
17422 TAA TAA TAT TTA TAA TAA TAA TAA TAA TAA TAT TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
17469 TGGATAAAAA
Statistics
Matches: 84, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 84 1.00
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:25004 original size:183 final size:183
Alignment explanation
Indices: 24635--25004 Score: 604
Period size: 183 Copynumber: 2.0 Consensus size: 183
24625 TTAAATATAT
*
24635 TATATAACATATAGGCTCACCCCAAACCATTTAAAACTCAATTAATAATTTAAGATCCAATAGCT
1 TATATAACATATAGGCTCACCCCAAACCATTTAAAACTCAATTAATAATTTAAGATCCAATAACT
24700 TTTAAACCTAAATCAATATTAATTAATTAAAAAATTATATAAAATTTTTATTTTATAATTATATA
66 TTTAAACCTAAATCAATATTAATTAATTAAAAAATTATATAAAATTTTTATTTTATAATTATATA
** *
24765 TTATTTAAATTAATTGTAAACTATTTTTTAATTAAAAAATATTAATTATATTA
131 TTATTTAAATTAATCATAAACTATTTTTTAATTAAAAAACATTAATTATATTA
*
24818 TATATAACATAT-GTGCTCAGCCCAAACCATTTAAAACTCAATTAATAATTTAAGATCCAATAAC
1 TATATAACATATAG-GCTCACCCCAAACCATTTAAAACTCAATTAATAATTTAAGATCCAATAAC
* * *
24882 TTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATTTGAAATTTTTATTTTATAATTCTA
65 TTTTAAACCTAAATCAATATTAATTAATTAAAAAA-TTATATAAAATTTTTATTTTATAATTATA
24947 TATTATTTAAATTAATCATAAACT-TTTTTTGAATTAAAAAACATTTAATT-T-TTA
129 TATTATTTAAATTAATCATAAACTATTTTTT-AATTAAAAAACA-TTAATTATATTA
25001 TATA
1 TATA
25005 AATTAGAAAA
Statistics
Matches: 175, Mismatches: 8, Indels: 8
0.92 0.04 0.04
Matches are distributed among these distances:
182 1 0.01
183 108 0.62
184 60 0.34
185 6 0.03
ACGTcount: A:0.45, C:0.10, G:0.03, T:0.42
Consensus pattern (183 bp):
TATATAACATATAGGCTCACCCCAAACCATTTAAAACTCAATTAATAATTTAAGATCCAATAACT
TTTAAACCTAAATCAATATTAATTAATTAAAAAATTATATAAAATTTTTATTTTATAATTATATA
TTATTTAAATTAATCATAAACTATTTTTTAATTAAAAAACATTAATTATATTA
Found at i:29362 original size:16 final size:16
Alignment explanation
Indices: 29337--29367 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29327 GACGAGTGCA
29337 GATGAACATCATTAAT
1 GATGAACATCATTAAT
*
29353 GATGAGCATCATTAA
1 GATGAACATCATTAA
29368 ATTATAAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (16 bp):
GATGAACATCATTAAT
Found at i:32317 original size:7 final size:8
Alignment explanation
Indices: 32306--32338 Score: 66
Period size: 8 Copynumber: 4.1 Consensus size: 8
32296 ATTTATTATT
32306 TTTTTTAA
1 TTTTTTAA
32314 TTTTTTAA
1 TTTTTTAA
32322 TTTTTTAA
1 TTTTTTAA
32330 TTTTTTAA
1 TTTTTTAA
32338 T
1 T
32339 ATTAAGTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TTTTTTAA
Found at i:37433 original size:16 final size:16
Alignment explanation
Indices: 37412--37443 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
37402 ATACCCGAAT
37412 GGTTGATGATGAGCTC
1 GGTTGATGATGAGCTC
37428 GGTTGATGATGAGCTC
1 GGTTGATGATGAGCTC
37444 CTTGATTGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.12, G:0.38, T:0.31
Consensus pattern (16 bp):
GGTTGATGATGAGCTC
Found at i:37453 original size:16 final size:16
Alignment explanation
Indices: 37414--37454 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
37404 ACCCGAATGG
*
37414 TTGATGATGAGCTCGG
1 TTGATGATGAGCTCGC
37430 TTGATGATGAGCTC-C
1 TTGATGATGAGCTCGC
37445 TTGATTGATG
1 TTGA-TGATG
37455 CGTGTTTTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 4 0.17
16 19 0.83
ACGTcount: A:0.20, C:0.12, G:0.32, T:0.37
Consensus pattern (16 bp):
TTGATGATGAGCTCGC
Found at i:39091 original size:53 final size:54
Alignment explanation
Indices: 38924--39398 Score: 432
Period size: 55 Copynumber: 8.8 Consensus size: 54
38914 TGGGTTCGCT
* *
38924 CCCTATTTCTTCAGAGGGTATAAGACTTGAATC-ATCTTCAACAAACTT--GTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGAC-CGAA-CAATCTTCAAC-AA-TTGCGTCTGCC
* * *
38979 CCCTATTTCTTCCGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTTTGCC
1 CCCTATTTCTTCAGAGAGTATAAGAC-CGAACAATCTTCAACAATTGCGTCTGCC
* * * * * *
39034 CCCTATTTCTTCCGAGAGTATAAGACC-CATAATCTTCATCAATCGCATCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACCGAACAATCTTCAACAATTGCGTCTGCC
** *
39087 CCCTATTTCTTCAGAGAGTATAAGATCCGAACAATCTTCAATGATTGTGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGA-CCGAACAATCTTCAACAATTGCGTCTGCC
* * * * * * *
39142 CCCTTTTTCTTCAGAGAGTATAAGACC-CACAATCTTCATCAATCGTGTTTGCT
1 CCCTATTTCTTCAGAGAGTATAAGACCGAACAATCTTCAACAATTGCGTCTGCC
*
39195 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGAC-CGAACAATCTTCAACAATTGCGTCTGCC
* * **
39250 CCCTATTTCTTCAGAGAGTATAAGACC-CACAATCTTCAACAATTGGGT-TCGTT
1 CCCTATTTCTTCAGAGAGTATAAGACCGAACAATCTTCAACAATTGCGTCT-GCC
* * * * * * * * * *
39303 CCCTCTTTCTCCAGGGAGTATAAAACTC-AAAAATCTTTTGAA-AA-CGTGTATGCT
1 CCCTATTTCTTCAGAGAGTATAAGAC-CGAACAATC--TTCAACAATTGCGTCTGCC
* *
39357 CCCTATTCCTTCAGAGAGTATAAGACC-CACAATCTTCAACAA
1 CCCTATTTCTTCAGAGAGTATAAGACCGAACAATCTTCAACAA
39399 ATGGGTTCGC
Statistics
Matches: 347, Mismatches: 60, Indels: 29
0.80 0.14 0.07
Matches are distributed among these distances:
51 4 0.01
52 3 0.01
53 136 0.39
54 41 0.12
55 159 0.46
56 4 0.01
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.31
Consensus pattern (54 bp):
CCCTATTTCTTCAGAGAGTATAAGACCGAACAATCTTCAACAATTGCGTCTGCC
Found at i:39306 original size:108 final size:108
Alignment explanation
Indices: 38979--39419 Score: 541
Period size: 108 Copynumber: 4.1 Consensus size: 108
38969 CTTGTCTGCC
* *
38979 CCCTATTTCTTCCGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTTTGCCCCCTATTTCT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCCCCCTATTTCT
* * * * ** *
39044 TCCGAGAGTATAAGACCCATAATCTTCATCAA-TCGCATCTGCC
66 TCAGAGAGTATAAGACCCACAATCTTCAACAATTGGGTTC-GCT
* * *
39087 CCCTATTTCTTCAGAGAGTATAAGA-TCCGAACAATCTTCAATGATTGTGTCTGCCCCCTTTTTC
1 CCCTATTTCTTCAGAGAGTATAAGACT-CGAACAATCTTCAACGATTGCGTCTGCCCCCTATTTC
* * * *
39151 TTCAGAGAGTATAAGACCCACAATCTTCATCAATCGTGTTTGCT
65 TTCAGAGAGTATAAGACCCACAATCTTCAACAATTGGGTTCGCT
39195 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCCCCCTATTTCT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCCCCCTATTTCT
*
39260 TCAGAGAGTATAAGACCCACAATCTTCAACAATTGGGTTCGTT
66 TCAGAGAGTATAAGACCCACAATCTTCAACAATTGGGTTCGCT
* * * * * * ** * * * *
39303 CCCTCTTTCTCCAGGGAGTATAAAACTC-AAAAATCTTTTGAA--AACGTGTATGCTCCCTATTC
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATC--TTCAACGATTGCGTCTGCCCCCTATTT
*
39365 CTTCAGAGAGTATAAGACCCACAATCTTCAACAAATGGGTTCGCT
64 CTTCAGAGAGTATAAGACCCACAATCTTCAACAATTGGGTTCGCT
39410 CCCTATTTCT
1 CCCTATTTCT
39420 CTAGGGAGTA
Statistics
Matches: 291, Mismatches: 37, Indels: 11
0.86 0.11 0.03
Matches are distributed among these distances:
107 73 0.25
108 212 0.73
109 6 0.02
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.32
Consensus pattern (108 bp):
CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCCCCCTATTTCT
TCAGAGAGTATAAGACCCACAATCTTCAACAATTGGGTTCGCT
Found at i:39571 original size:51 final size:51
Alignment explanation
Indices: 39396--39903 Score: 594
Period size: 51 Copynumber: 9.8 Consensus size: 51
39386 CAATCTTCAA
* * * * * *
39396 CAAATGGGTTCGCTCCCTATTTCTCTAGGGAGTAT-GAAACTCAGACATATTCTT
1 CAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAG-AACTC-GA-ACA-TCTT
** * *
39450 CAAACGGGTTCGCTCCCCCTTTCTCTAGGGAGTATAGAACTCGAACATCTCTT
1 CAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACA--TCTT
**
39503 CAAACGGGTTCGCTCCTTCCCTCTTTAAGGAGTATAGAACTCGAACATCTT
1 CAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTT
39554 CAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTT
1 CAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTT
* * *
39605 CAAATGGGTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACTCGAACATCTCTT
1 CAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACA--TCTT
* * * * *
39658 C--ACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGGACTCGAACATCTT
1 CAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTT
*
39707 C-AACTGGGTTCGCTCCTTCTTTCTTTAAGGAGTATGGAACTCGAACATCTT
1 CAAAC-GGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTT
* * *
39758 TAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGCATATCTT
1 CAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTT
* * * * *
39809 CACACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTC-AGACATCTCTT
1 CAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGA-ACA--TCTT
* *
39862 CAAACGGGTTCACTCCTTCTTTCTTTAAGGAGTATGGAACTC
1 CAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTC
39904 AAATAATCTT
Statistics
Matches: 403, Mismatches: 41, Indels: 21
0.87 0.09 0.05
Matches are distributed among these distances:
49 5 0.01
50 2 0.00
51 260 0.65
52 5 0.01
53 93 0.23
54 37 0.09
55 1 0.00
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.32
Consensus pattern (51 bp):
CAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTT
Found at i:39731 original size:153 final size:153
Alignment explanation
Indices: 39396--39903 Score: 682
Period size: 153 Copynumber: 3.3 Consensus size: 153
39386 CAATCTTCAA
* * * * * * *
39396 CAAATGGGTTCGCTCCCTATTTCTCTAGGGAGTATGAAACTCAGACATATTCTTCAAACGGGTTC
1 CAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATGGAACTC-GA-ACA-TCTTCAAACGGGTTC
* * * **
39461 GCTCCCCCTTTCTCTAGGGAGTATAGAACTCGAACATCTCTTCAAACGGGTTCGCTCCTTCCCTC
63 GCTCCCTCTTTCTTTAGGGAGTATAGAACTCGAACATCTCTTC--ACGGGTTCGCTCCCTCTTTC
* * *
39526 TTTAAGGAGTATAGAACTCGAACATCTT
126 TCTAGGGAGTATGGAACTCGAACATCTT
* *
39554 CAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTTCAAATGGGTTCGCT
1 CAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATGGAACTCGAACATCTTCAAACGGGTTCGCT
39619 CCCTCTTTCTTTAGGGAGTATAGAACTCGAACATCTCTTCACGGGTTCGCTCCCTCTTTCTCTAG
66 CCCTCTTTCTTTAGGGAGTATAGAACTCGAACATCTCTTCACGGGTTCGCTCCCTCTTTCTCTAG
*
39684 GGAGTATGGGACTCGAACATCTT
131 GGAGTATGGAACTCGAACATCTT
*
39707 C-AACTGGGTTCGCTCCTTCTTTCTTTAAGGAGTATGGAACTCGAACATCTTTAAACGGGTTCGC
1 CAAAC-GGGTTCGCTCCTTCTTTCTTTAAGGAGTATGGAACTCGAACATCTTCAAACGGGTTCGC
* * *
39771 TCCTTCTTTCTTTAAGGAGTATAGAACTCG--CATATCTTCACACGGGTTCGCTCCCTCTTTCTC
65 TCCCTCTTTCTTTAGGGAGTATAGAACTCGAACATCTCTT--CACGGGTTCGCTCCCTCTTTCTC
39834 TAGGGAGTATGGAACTC-AGACATCTCTT
128 TAGGGAGTATGGAACTCGA-ACA--TCTT
*
39862 CAAACGGGTTCACTCCTTCTTTCTTTAAGGAGTATGGAACTC
1 CAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATGGAACTC
39904 AAATAATCTT
Statistics
Matches: 317, Mismatches: 26, Indels: 17
0.88 0.07 0.05
Matches are distributed among these distances:
151 7 0.02
152 4 0.01
153 168 0.53
155 96 0.30
156 5 0.02
157 2 0.01
158 35 0.11
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.32
Consensus pattern (153 bp):
CAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATGGAACTCGAACATCTTCAAACGGGTTCGCT
CCCTCTTTCTTTAGGGAGTATAGAACTCGAACATCTCTTCACGGGTTCGCTCCCTCTTTCTCTAG
GGAGTATGGAACTCGAACATCTT
Found at i:40350 original size:36 final size:36
Alignment explanation
Indices: 40303--40474 Score: 182
Period size: 36 Copynumber: 4.8 Consensus size: 36
40293 AAAATGGATA
* * *
40303 TGCTTCACTACTTTTTGGTGAGGACTTAAGATGGTT
1 TGCTTCACTACTCTCTGGTGAAGACTTAAGATGGTT
*
40339 TGCTTCACTACTCTCTGGTGAAGACTTATGATGGTT
1 TGCTTCACTACTCTCTGGTGAAGACTTAAGATGGTT
* ** * * * *
40375 TGCTTCACTATTCTCCAGTGAAGGCTTCAGATTGAT
1 TGCTTCACTACTCTCTGGTGAAGACTTAAGATGGTT
* * * *
40411 TGCTTCACTATTCTCCGGTGAAGGCTTCAGATGGTT
1 TGCTTCACTACTCTCTGGTGAAGACTTAAGATGGTT
* * *
40447 TGCTTCACTATTCTCCGGTGAAGGCTTA
1 TGCTTCACTACTCTCTGGTGAAGACTTA
40475 GGATTGACTT
Statistics
Matches: 120, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 120 1.00
ACGTcount: A:0.19, C:0.20, G:0.23, T:0.38
Consensus pattern (36 bp):
TGCTTCACTACTCTCTGGTGAAGACTTAAGATGGTT
Found at i:40420 original size:72 final size:72
Alignment explanation
Indices: 40338--40481 Score: 220
Period size: 72 Copynumber: 2.0 Consensus size: 72
40328 TTAAGATGGT
*
40338 TTGCTTCACTACTCTCTGGTGAAGACTT-ATGATGGTTTGCTTCACTATTCTCCAGTGAAGGCTT
1 TTGCTTCACTACTCTCCGGTGAAGACTTCA-GATGGTTTGCTTCACTATTCTCCAGTGAAGGCTT
40402 CA-GATTGA
65 -AGGATTGA
* * *
40410 TTGCTTCACTATTCTCCGGTGAAGGCTTCAGATGGTTTGCTTCACTATTCTCCGGTGAAGGCTTA
1 TTGCTTCACTACTCTCCGGTGAAGACTTCAGATGGTTTGCTTCACTATTCTCCAGTGAAGGCTTA
40475 GGATTGA
66 GGATTGA
40482 CTTTGCTCCA
Statistics
Matches: 66, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
71 1 0.02
72 64 0.97
73 1 0.02
ACGTcount: A:0.19, C:0.21, G:0.23, T:0.37
Consensus pattern (72 bp):
TTGCTTCACTACTCTCCGGTGAAGACTTCAGATGGTTTGCTTCACTATTCTCCAGTGAAGGCTTA
GGATTGA
Found at i:48423 original size:16 final size:16
Alignment explanation
Indices: 48402--48433 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
48392 ATACCCGAAT
48402 GGTTGATGATGAGCTC
1 GGTTGATGATGAGCTC
48418 GGTTGATGATGAGCTC
1 GGTTGATGATGAGCTC
48434 CTTGATTGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.12, G:0.38, T:0.31
Consensus pattern (16 bp):
GGTTGATGATGAGCTC
Found at i:48443 original size:16 final size:16
Alignment explanation
Indices: 48404--48444 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
48394 ACCCGAATGG
*
48404 TTGATGATGAGCTCGG
1 TTGATGATGAGCTCGC
48420 TTGATGATGAGCTC-C
1 TTGATGATGAGCTCGC
48435 TTGATTGATG
1 TTGA-TGATG
48445 CGTGTTTTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 4 0.17
16 19 0.83
ACGTcount: A:0.20, C:0.12, G:0.32, T:0.37
Consensus pattern (16 bp):
TTGATGATGAGCTCGC
Found at i:50103 original size:20 final size:21
Alignment explanation
Indices: 50078--50119 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
50068 AAATAACATT
* *
50078 TATTTT-TTGTATTTAATAAA
1 TATTTTATTGCATTTAAGAAA
50098 TATTTTATTGCATTTAAGAAA
1 TATTTTATTGCATTTAAGAAA
50119 T
1 T
50120 TGTGTATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.36, C:0.02, G:0.07, T:0.55
Consensus pattern (21 bp):
TATTTTATTGCATTTAAGAAA
Found at i:50738 original size:2 final size:2
Alignment explanation
Indices: 50727--50788 Score: 117
Period size: 2 Copynumber: 31.5 Consensus size: 2
50717 TATGATTAAA
50727 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
50768 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
50789 AGTATATGAA
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 58 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:51680 original size:3 final size:3
Alignment explanation
Indices: 51674--51699 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
51664 GAAAAAAATC
51674 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
51700 TGTCATCACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:54422 original size:21 final size:21
Alignment explanation
Indices: 54383--54422 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
54373 TTTTTTTCCA
* *
54383 ATGATGATATGTCATTACATT
1 ATGATGACATGTCAGTACATT
*
54404 ATGATGACATGTTAGTACA
1 ATGATGACATGTCAGTACA
54423 CTTTGACGAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.38
Consensus pattern (21 bp):
ATGATGACATGTCAGTACATT
Found at i:54890 original size:20 final size:22
Alignment explanation
Indices: 54852--54892 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 22
54842 ATTTAAAAAA
54852 AATTATATTATTATTAAATTTT
1 AATTATATTATTATTAAATTTT
54874 AATTA-ATTATT-TTAAATTT
1 AATTATATTATTATTAAATTT
54893 CTAAAAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.42
21 6 0.32
22 5 0.26
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
AATTATATTATTATTAAATTTT
Found at i:55468 original size:2 final size:2
Alignment explanation
Indices: 55461--55535 Score: 132
Period size: 2 Copynumber: 37.5 Consensus size: 2
55451 TTAGAGTAAA
55461 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
55503 AT AT AT AT AT AT AT AT AT AT AC AT AC AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
55536 CACCAAATAA
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:55613 original size:20 final size:20
Alignment explanation
Indices: 55553--55648 Score: 70
Period size: 20 Copynumber: 4.8 Consensus size: 20
55543 TAAGTCAAAG
* *
55553 GGAAAAAAGGAGAAAGAAAAA
1 GGAAAAAATGA-AAAAAAAAA
* *
55574 GGAAAAAAAT-AATAATAAAA
1 GG-AAAAAATGAAAAAAAAAA
55594 GGAAAAAATGAAAAAAAAAA
1 GGAAAAAATGAAAAAAAAAA
** * *
55614 TTAAAAGAT-AAATGAAAAAA
1 GGAAAAAATGAAA-AAAAAAA
*
55634 GTAAAAAATGAAAAA
1 GGAAAAAATGAAAAA
55649 GTTTTTTTTA
Statistics
Matches: 58, Mismatches: 13, Indels: 9
0.73 0.16 0.11
Matches are distributed among these distances:
19 10 0.17
20 36 0.62
21 6 0.10
22 6 0.10
ACGTcount: A:0.74, C:0.00, G:0.16, T:0.10
Consensus pattern (20 bp):
GGAAAAAATGAAAAAAAAAA
Found at i:55613 original size:40 final size:40
Alignment explanation
Indices: 55553--55648 Score: 97
Period size: 40 Copynumber: 2.4 Consensus size: 40
55543 TAAGTCAAAG
* *
55553 GGAAAAAAGGAGAAAGAAAAAGGAAAAAAAT-AAT-AATAAAA
1 GGAAAAAATGA-AAA-AAAAAAGAAAAAAATAAATGAA-AAAA
** *
55594 GGAAAAAATGAAAAAAAAAATTAAAAGATAAATGAAAAAA
1 GGAAAAAATGAAAAAAAAAAGAAAAAAATAAATGAAAAAA
*
55634 GTAAAAAATGAAAAA
1 GGAAAAAATGAAAAA
55649 GTTTTTTTTA
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
39 11 0.23
40 24 0.51
41 12 0.26
ACGTcount: A:0.74, C:0.00, G:0.16, T:0.10
Consensus pattern (40 bp):
GGAAAAAATGAAAAAAAAAAGAAAAAAATAAATGAAAAAA
Found at i:55779 original size:14 final size:14
Alignment explanation
Indices: 55760--55800 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
55750 AATAAAAATG
55760 AAATGAAATAACAA
1 AAATGAAATAACAA
55774 AAATGAAAT-A-AA
1 AAATGAAATAACAA
55786 AAAT-AAATAAACAA
1 AAATGAAAT-AACAA
55800 A
1 A
55801 TATATATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
11 4 0.17
12 6 0.25
13 2 0.08
14 12 0.50
ACGTcount: A:0.76, C:0.05, G:0.05, T:0.15
Consensus pattern (14 bp):
AAATGAAATAACAA
Found at i:57027 original size:39 final size:39
Alignment explanation
Indices: 56935--57339 Score: 304
Period size: 39 Copynumber: 10.6 Consensus size: 39
56925 ATTATAATAT
* * *
56935 AAACTATATATTATATATAA-GTTTTCAAAAACG-TTTAA
1 AAACTATATAATATATA-AATATTTTCAAAAATGTTTTAA
* * * * *
56973 AAATTATAAAATATATAAATGTTTTCGAAAATGTTTTCA
1 AAACTATATAATATATAAATATTTTCAAAAATGTTTTAA
*
57012 AAACTATATAATATAT-AA-GTTTTCAAAAATGTTTTCAA
1 AAACTATATAATATATAAATATTTTCAAAAATGTTTT-AA
* * * *
57050 AAACTATAT-AT-TATATATATTTTAAAAAATATTTTCA
1 AAACTATATAATATATAAATATTTTCAAAAATGTTTTAA
* *
57087 AAACTATAT-A-ATAT--ATGTTTTCAAAAATGATTTCAAA
1 AAACTATATAATATATAAATATTTTCAAAAATG-TTT-TAA
* *
57124 AAACTATGT-AT-TATATAT-TTTTC-AAAATGATTTTAA
1 AAACTATATAATATATAAATATTTTCAAAAATG-TTTTAA
* * *
57160 AAAATATATACATATATTATATATATATTCTAAAATGTTTTAA
1 AAACTATATA-ATATA-TA-A-ATATTTTCAAAAATGTTTTAA
* * *
57203 AAACTATA-CAT-TATATA-ATTTTCAAAAATATTTTTAA
1 AAACTATATAATATATAAATATTTTCAAAAAT-GTTTTAA
*
57240 AAACTATATAATATATATATATTTTCAAAAATGTTTTAA
1 AAACTATATAATATATAAATATTTTCAAAAATGTTTTAA
* * * *** **
57279 AAATTATATATTATATACATATTTTCAAAAACCATTTGT
1 AAACTATATAATATATAAATATTTTCAAAAATGTTTTAA
*
57318 AAACTATATAATATATAGATAT
1 AAACTATATAATATATAAATAT
57340 ATATGTATAT
Statistics
Matches: 299, Mismatches: 45, Indels: 45
0.77 0.12 0.12
Matches are distributed among these distances:
35 12 0.04
36 25 0.08
37 73 0.24
38 60 0.20
39 86 0.29
40 16 0.05
41 2 0.01
42 2 0.01
43 17 0.06
44 6 0.02
ACGTcount: A:0.47, C:0.07, G:0.04, T:0.42
Consensus pattern (39 bp):
AAACTATATAATATATAAATATTTTCAAAAATGTTTTAA
Found at i:57034 original size:37 final size:37
Alignment explanation
Indices: 56935--57334 Score: 319
Period size: 37 Copynumber: 10.5 Consensus size: 37
56925 ATTATAATAT
*
56935 AAACTATATATTATATATAAGTTTTCAAAAACG-TTTAA
1 AAACTATATA--ATATATAAGTTTTCAAAAATGTTTTAA
* * * *
56973 AAATTATAAAATATATAAATGTTTTCGAAAATGTTTTCA
1 AAACTATATAATATAT-AA-GTTTTCAAAAATGTTTTAA
57012 AAACTATATAATATATAAGTTTTCAAAAATGTTTTCAA
1 AAACTATATAATATATAAGTTTTCAAAAATGTTTT-AA
* * * *
57050 AAACTATATATTATATATA-TTTTAAAAAATATTTTCA
1 AAACTATATAATATATA-AGTTTTCAAAAATGTTTTAA
*
57087 AAACTATATAATATAT--GTTTTCAAAAATGATTTCAAA
1 AAACTATATAATATATAAGTTTTCAAAAATG-TTT-TAA
* * *
57124 AAACTATGTATTATAT-ATTTTTC-AAAATGATTTTAA
1 AAACTATATAATATATAAGTTTTCAAAAATG-TTTTAA
* * *
57160 AAAATATATACATATATTATATATATATTCTAAAATGTTTTAA
1 AAACTATATA-ATATA-TA-A-GT-T-TTCAAAAATGTTTTAA
* * *
57203 AAACTATACATTATATAA-TTTTCAAAAATATTTTTAA
1 AAACTATATAATATATAAGTTTTCAAAAAT-GTTTTAA
*
57240 AAACTATATAATATATATATATTTTCAAAAATGTTTTAA
1 AAACTATATAATATATA-A-GTTTTCAAAAATGTTTTAA
* * * *** **
57279 AAATTATATATTATATACATATTTTCAAAAACCATTTGT
1 AAACTATATAATATATA-A-GTTTTCAAAAATGTTTTAA
57318 AAACTATATAATATATA
1 AAACTATATAATATATA
57335 GATATATATG
Statistics
Matches: 297, Mismatches: 44, Indels: 41
0.78 0.12 0.11
Matches are distributed among these distances:
35 10 0.03
36 27 0.09
37 85 0.29
38 60 0.20
39 71 0.24
40 13 0.04
41 3 0.01
42 5 0.02
43 17 0.06
44 6 0.02
ACGTcount: A:0.47, C:0.07, G:0.04, T:0.42
Consensus pattern (37 bp):
AAACTATATAATATATAAGTTTTCAAAAATGTTTTAA
Found at i:57218 original size:116 final size:119
Alignment explanation
Indices: 56968--57288 Score: 321
Period size: 116 Copynumber: 2.8 Consensus size: 119
56958 TTCAAAAACG
* * * *
56968 TTTAAAAATTATAAAATATATAAATGTTTTCGAAAATGTTTTC--AAAACTATATAATATATA-A
1 TTTAAAAACTATACAATATAT-AA--TTTTCAAAAAT-ATTTCAAAAAACTATATAATATATATA
* *
57030 -GTTTTCAAAAATGTTTTCAAAAACTATAT--AT-TA-TATATAT-T-TTAAAAAATAT
62 TATTTTCAAAAATGTTTT-AAAAAATATATACATATATTATATATATATTAAAAAATAT
* * * *
57082 TTTCAAAACTATATAATATAT-GTTTTCAAAAATGATTTCAAAAAACTATGT-AT-TATATAT-T
1 TTTAAAAACTATACAATATATAATTTTCAAAAAT-ATTTCAAAAAACTATATAATATATATATAT
** *
57143 TTTC-AAAATGATTTTAAAAAATATATACATATATTATATATATATTCTAAAATGT
65 TTTCAAAAATG-TTTTAAAAAATATATACATATATTATATATATATTAAAAAATAT
* **
57198 TTTAAAAACTATACATTATATAATTTTCAAAAATATTTTTAAAAACTATATAATATATATATATT
1 TTTAAAAACTATACAATATATAATTTTCAAAAATATTTCAAAAAACTATATAATATATATATATT
*
57263 TTCAAAAATGTTTTAAAAATTATATA
66 TTCAAAAATGTTTTAAAAAATATATA
57289 TTATATACAT
Statistics
Matches: 172, Mismatches: 19, Indels: 27
0.79 0.09 0.12
Matches are distributed among these distances:
110 35 0.20
111 12 0.07
112 11 0.06
113 2 0.01
114 25 0.15
115 1 0.01
116 40 0.23
117 13 0.08
118 7 0.04
119 20 0.12
120 6 0.03
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.43
Consensus pattern (119 bp):
TTTAAAAACTATACAATATATAATTTTCAAAAATATTTCAAAAAACTATATAATATATATATATT
TTCAAAAATGTTTTAAAAAATATATACATATATTATATATATATTAAAAAATAT
Found at i:58714 original size:19 final size:19
Alignment explanation
Indices: 58690--58733 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
58680 TTGACTATTG
58690 GTGTCAGTCAAAAGGTACA
1 GTGTCAGTCAAAAGGTACA
*
58709 GTGTCAGTCAAAAGGTATA
1 GTGTCAGTCAAAAGGTACA
58728 GTGTCA
1 GTGTCA
58734 AAAATGAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.34, C:0.14, G:0.27, T:0.25
Consensus pattern (19 bp):
GTGTCAGTCAAAAGGTACA
Found at i:70912 original size:20 final size:18
Alignment explanation
Indices: 70887--70930 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 18
70877 TTCACGTTCG
70887 AATAATAGTTTATT-ATTAA
1 AATAATA-TTT-TTAATTAA
70906 TAATAATATTTTTAATTAA
1 -AATAATATTTTTAATTAA
70925 AATAAT
1 AATAAT
70931 GGAATTTTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 8 0.35
19 8 0.35
20 7 0.30
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (18 bp):
AATAATATTTTTAATTAA
Found at i:75561 original size:29 final size:29
Alignment explanation
Indices: 75528--75586 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
75518 TTATGACCCC
75528 TATTTT-ATACTAATCCCTAAACTTTTGAA
1 TATTTTGAT-CTAATCCCTAAACTTTTGAA
* * *
75557 TATTTTGATTTCATCGCTAAACTTTTGAA
1 TATTTTGATCTAATCCCTAAACTTTTGAA
75586 T
1 T
75587 GTTCCAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 24 0.92
30 2 0.08
ACGTcount: A:0.31, C:0.15, G:0.07, T:0.47
Consensus pattern (29 bp):
TATTTTGATCTAATCCCTAAACTTTTGAA
Found at i:75596 original size:29 final size:29
Alignment explanation
Indices: 75540--75616 Score: 91
Period size: 29 Copynumber: 2.7 Consensus size: 29
75530 TTTTATACTA
* ***
75540 ATCCCTAAACTTTTGAATATTTTGATTTC
1 ATCCCTAAACTTTTGAATGTTCCAATTTC
*
75569 ATCGCTAAACTTTTGAATGTTCCAATTTC
1 ATCCCTAAACTTTTGAATGTTCCAATTTC
* *
75598 ATCCCCAAACTTTAGAATG
1 ATCCCTAAACTTTTGAATG
75617 ATCTAGGGGG
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.30, C:0.21, G:0.09, T:0.40
Consensus pattern (29 bp):
ATCCCTAAACTTTTGAATGTTCCAATTTC
Found at i:76079 original size:19 final size:19
Alignment explanation
Indices: 76027--76079 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
76017 AAAATATTTT
* *
76027 TTTTAAACTTTTTTTAAAA
1 TTTTAAAATATTTTTAAAA
* *
76046 TTTTTAAATAATTTT-AAA
1 TTTTAAAATATTTTTAAAA
76064 TTTTAAAAATATTTTT
1 TTTT-AAAATATTTTT
76080 TTTTTTTTTA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
18 7 0.26
19 20 0.74
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (19 bp):
TTTTAAAATATTTTTAAAA
Found at i:93870 original size:2 final size:2
Alignment explanation
Indices: 93865--93893 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
93855 AGAGAGAATT
93865 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
93894 TTTAAAAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:99846 original size:27 final size:27
Alignment explanation
Indices: 99795--99847 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
99785 TATTTCAATC
* **
99795 GATTTTATTATTGTTGGACGTTTTATT
1 GATTTTATTATTGTTGAACACTTTATT
*
99822 GATTTTGTTATTGTTGAACACTTTAT
1 GATTTTATTATTGTTGAACACTTTAT
99848 CGAAAATATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.21, C:0.06, G:0.17, T:0.57
Consensus pattern (27 bp):
GATTTTATTATTGTTGAACACTTTATT
Found at i:99894 original size:20 final size:21
Alignment explanation
Indices: 99857--99900 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 21
99847 TCGAAAATAT
99857 TAAAAAAATTAATATTTTAAA
1 TAAAAAAATTAATATTTTAAA
99878 TAAAAATAA-TAAT-TTTTAAA
1 TAAAAA-AATTAATATTTTAAA
99898 TAA
1 TAA
99901 TTTTTTATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 10 0.45
21 10 0.45
22 2 0.09
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
TAAAAAAATTAATATTTTAAA
Found at i:101425 original size:26 final size:26
Alignment explanation
Indices: 101396--101447 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
101386 TTTAGTGTCT
101396 CATCCTACTAAACTAATTAATTGTTG
1 CATCCTACTAAACTAATTAATTGTTG
101422 CATCCTACTAAACTAATTAATTGTTG
1 CATCCTACTAAACTAATTAATTGTTG
101448 GTAAAACAAT
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:0.35, C:0.19, G:0.08, T:0.38
Consensus pattern (26 bp):
CATCCTACTAAACTAATTAATTGTTG
Found at i:109861 original size:2 final size:2
Alignment explanation
Indices: 109856--109901 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
109846 CATTTATAGT
109856 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
109898 TA TA
1 TA TA
109902 GGGGTGTAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:110132 original size:17 final size:17
Alignment explanation
Indices: 110110--110209 Score: 79
Period size: 17 Copynumber: 6.2 Consensus size: 17
110100 TGATTTTGAG
110110 CTCGATTCAAGCTCGAA
1 CTCGATTCAAGCTCGAA
110127 CTCGATTCAAGCTCGAA
1 CTCGATTCAAGCTCGAA
* * * * *
110144 CTCAAACTCGAA-TTTGAG
1 CTC-GATTC-AAGCTCGAA
*
110162 CTTGATTCAAGCT----
1 CTCGATTCAAGCTCGAA
110175 CT--ATTCAAGCTCGAA
1 CTCGATTCAAGCTCGAA
110190 CTCGATTCAAGCTCGAA
1 CTCGATTCAAGCTCGAA
110207 CTC
1 CTC
110210 AAACTCGAAT
Statistics
Matches: 65, Mismatches: 9, Indels: 18
0.71 0.10 0.20
Matches are distributed among these distances:
11 9 0.14
13 2 0.03
15 2 0.03
16 2 0.03
17 40 0.62
18 8 0.12
19 2 0.03
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (17 bp):
CTCGATTCAAGCTCGAA
Found at i:110205 original size:11 final size:11
Alignment explanation
Indices: 110085--110188 Score: 56
Period size: 11 Copynumber: 9.6 Consensus size: 11
110075 AAAATTCAAG
*
110085 AGCTCGATTGA
1 AGCTCGATTCA
* **
110096 AGCTTGATTTTG
1 AGCTCGA-TTCA
110108 AGCTCGATTCA
1 AGCTCGATTCA
110119 AGCTCG----A
1 AGCTCGATTCA
110126 A-CTCGATTCA
1 AGCTCGATTCA
*
110136 AGCTCGAACTCA
1 AGCTCG-ATTCA
* **
110148 AACTCGAATTTG
1 AGCTCG-ATTCA
*
110160 AGCTTGATTCA
1 AGCTCGATTCA
*
110171 AGCTCTATTCA
1 AGCTCGATTCA
110182 AGCTCGA
1 AGCTCGA
110189 ACTCGATTCA
Statistics
Matches: 68, Mismatches: 18, Indels: 14
0.68 0.18 0.14
Matches are distributed among these distances:
6 4 0.06
7 2 0.03
10 2 0.03
11 36 0.53
12 24 0.35
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (11 bp):
AGCTCGATTCA
Done.