Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008816.1 Hibiscus syriacus cultivar Beakdansim tig00111981_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: 92171
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3270 original size:28 final size:26
Alignment explanation
Indices: 3214--3280 Score: 84
Period size: 28 Copynumber: 2.6 Consensus size: 26
3204 TTTTTACCCA
3214 TTAAAATTTTATA--AATTCTCCTAT
1 TTAAAATTTTATATGAATTCTCCTAT
* *
3238 GTAAAATTTTATATGAGTTCTCCCCTAT
1 TTAAAATTTTATATGAATTCT--CCTAT
3266 TTAAAATTTTATATG
1 TTAAAATTTTATATG
3281 TTTGACCCTC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
24 12 0.33
26 5 0.14
28 19 0.53
ACGTcount: A:0.34, C:0.12, G:0.06, T:0.48
Consensus pattern (26 bp):
TTAAAATTTTATATGAATTCTCCTAT
Found at i:4517 original size:2 final size:2
Alignment explanation
Indices: 4510--4544 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
4500 ATTTAAACAA
*
4510 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4545 GACTAATATA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Found at i:5874 original size:3 final size:3
Alignment explanation
Indices: 5866--5927 Score: 81
Period size: 3 Copynumber: 21.0 Consensus size: 3
5856 AATTATTTCT
* * *
5866 TAA TAA TAA TAA TAA TAA -AA TAA TTA TAA TAA TAA TTA TTA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
5913 TAA TAA AAA TAA TAA
1 TAA TAA TAA TAA TAA
5928 AACCGGGATA
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
2 2 0.04
3 50 0.96
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:6319 original size:123 final size:122
Alignment explanation
Indices: 6189--6762 Score: 839
Period size: 123 Copynumber: 4.7 Consensus size: 122
6179 AGCTAAAGTC
* * *
6189 GAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTCTTCAGATGAATTCTTCTCATTATGAAC-T
1 GAACAAGTTCTTCTCATTATGAACTTTTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTT
* * * * * *
6253 CTACCTGAAAATGGCT-CTGCTGCTCTATCTCCTTTTGTGATAGAATCGAGCAAAGGGTT
66 CT--CTGGAAAT-GTTGATGCTGATCTATCTCCTTCTGTGATAGAATCGAGCAAAAGGTT
* * *
6312 GAACAAGTTCTTCTTATTATAAAC-TTTACATTCCTCTTCAGATGAGTTCTTCTCATTATGAACT
1 GAACAAGTTCTTCTCATTATGAACTTTTTC-TTCCTCTTCAGATGAGTTCTTCTCATTATGAAC-
*
6376 TTCTCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAAAATCGAGCAAAAGGTT
64 TTCTCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAATCGAGCAAAAGGTT
* *
6435 GAACAAGTTCTTCTCATTATGAACTTTTTCTTCCTTTTCAGATGAGTTCTTCTCATTATTAACTT
1 GAACAAGTTCTTCTCATTATGAACTTTTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTT
* *
6500 CCTCTGGAAATGTTGATGCTGATTTATCTCCTTATGTGATAGAATCGAGCAAAAGGTT
66 -CTCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAATCGAGCAAAAGGTT
*
6558 AAACAAGTTCTTCTCATTATGAACTTTTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTT
1 GAACAAGTTCTTCTCATTATGAACTTTTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTT
* *
6623 CCTTTGGAAATGTTAATGCTGATCTATCTCCTTCTGTGATAGAATCGAGCAAAAGGTT
66 -CTCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAATCGAGCAAAAGGTT
* * *
6681 GAACAAGTTCTTCCCATTATGAACTTTTTCTTCCTTTTCAGATGAGTTTTTCTCATTATGAACTC
1 GAACAAGTTCTTCTCATTATGAACTTTTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACT-
*
6746 TTTCTGGAAATGTTGAT
65 TCTCTGGAAATGTTGAT
6763 CCATCGAGTG
Statistics
Matches: 411, Mismatches: 33, Indels: 14
0.90 0.07 0.03
Matches are distributed among these distances:
122 7 0.02
123 396 0.96
124 5 0.01
125 3 0.01
ACGTcount: A:0.25, C:0.19, G:0.15, T:0.40
Consensus pattern (122 bp):
GAACAAGTTCTTCTCATTATGAACTTTTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTT
CTCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAATCGAGCAAAAGGTT
Found at i:6927 original size:36 final size:36
Alignment explanation
Indices: 6801--6927 Score: 128
Period size: 36 Copynumber: 3.5 Consensus size: 36
6791 AGTAAAACTG
* *
6801 TCTCAAGCGAGACGAATCTTGTTTTAAGAAAAAAAA
1 TCTCAAGCGAGACAAATTTTGTTTTAAGAAAAAAAA
* * * ** ***
6837 TCTCAAGGGAGATAAATTATTGTTTTGAGTGAAATTG
1 TCTCAAGCGAGACAAATT-TTGTTTTAAGAAAAAAAA
*
6874 TCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAA
1 TCTCAAGCGAGACAAATTTTGTTTTAAGAAAAAAAA
* *
6910 TCTCAAGTGAGATAAATT
1 TCTCAAGCGAGACAAATT
6928 GTATTTGAAA
Statistics
Matches: 70, Mismatches: 20, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
36 42 0.60
37 28 0.40
ACGTcount: A:0.40, C:0.11, G:0.18, T:0.31
Consensus pattern (36 bp):
TCTCAAGCGAGACAAATTTTGTTTTAAGAAAAAAAA
Found at i:7678 original size:22 final size:22
Alignment explanation
Indices: 7623--7679 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
7613 AATAAAATTT
* * *
7623 TCATTTTTGAAAAGAGACTCTA
1 TCATCTTTGAAGAGAGAATCTA
7645 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
7667 TCATCTTTGAAGA
1 TCATCTTTGAAGA
7680 ATGTAGATGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAGAGAGAATCTA
Found at i:8302 original size:204 final size:208
Alignment explanation
Indices: 7902--8320 Score: 562
Period size: 204 Copynumber: 2.0 Consensus size: 208
7892 TCTTGTTGTT
* * * * *
7902 AAAATTTCAGTTTCCCTTCTATGGAAAGAAATCTTCATCATATCTCACTTCTAACCTTGGGGTTT
1 AAAATTTAAGCTTCCCTTATATGGAAAGAAATCTTCATCATATCTCACTTCTAACCTTGGGGGTA
*
7967 AAGAAGAAAAACTTCATCTTGCATCAATAAATGAAAATCATATGATCATAACATTGGTTCAGCAC
66 AAGAAGAAAAACTTCATCTTGCATCAATAAATG--AA-CATATGATCAT-A-ATTAGTTCAGCAC
* ** * *
8032 CATAATCATTGGTTCATAAAACATTTGGCAATGCATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
126 CATAATCACTGGTTCATAAAACATTTGGCAACACATTCATCATTTCCTATGGCTTCTGCTCAGAT
8097 GTTCGTAAAACATTTGAC
191 GTTCGTAAAACATTTGAC
* *
8115 AAAATTTAAGCTTCCCTTATGTGGAAAGAAATCTTCATTATATCTCACTTCTAACCTTGGGGGTA
1 AAAATTTAAGCTTCCCTTATATGGAAAGAAATCTTCATCATATCTCACTTCTAACCTTGGGGGTA
* * ** *
8180 AATAAGTCAAAA-TTCATCTTGGGTCCATAAATTG-A-A-AT-ATCAT-ATTAGTTCAGCACCAT
66 AAGAAG-AAAAACTTCATCTTGCATCAATAAA-TGAACATATGATCATAATTAGTTCAGCACCAT
*
8239 AATCACTGGTTCATAAAACATTTGGCAACACATTCATCATTTCCTATTGCTTCTGCTCAGATGTT
129 AATCACTGGTTCATAAAACATTTGGCAACACATTCATCATTTCCTATGGCTTCTGCTCAGATGTT
8304 CGTAAAACATTTGAC
194 CGTAAAACATTTGAC
8319 AA
1 AA
8321 CACATTCATC
Statistics
Matches: 185, Mismatches: 19, Indels: 13
0.85 0.09 0.06
Matches are distributed among these distances:
204 91 0.49
207 5 0.03
208 2 0.01
209 1 0.01
211 1 0.01
213 79 0.43
214 6 0.03
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.34
Consensus pattern (208 bp):
AAAATTTAAGCTTCCCTTATATGGAAAGAAATCTTCATCATATCTCACTTCTAACCTTGGGGGTA
AAGAAGAAAAACTTCATCTTGCATCAATAAATGAACATATGATCATAATTAGTTCAGCACCATAA
TCACTGGTTCATAAAACATTTGGCAACACATTCATCATTTCCTATGGCTTCTGCTCAGATGTTCG
TAAAACATTTGAC
Found at i:8316 original size:54 final size:53
Alignment explanation
Indices: 8247--8572 Score: 354
Period size: 54 Copynumber: 6.1 Consensus size: 53
8237 ATAATCACTG
* *
8247 GTTCATAAAACATTTGGCAACACATTCATCATTTCCTAT-TGCTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCATTT-C-ATGTGCTTCTGCTCAGAT
* * *
8301 GTTCGTAAAACATTTGACAACACATTCATCATTTCATGTGTTTCTACACAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCATTTCATGTGCTTCTGCTCAGAT
* *
8354 GTTCTTCAAACATTTGACAACACATTCATCATTTCATGTGTCTTCTG-TACAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCATTTCATGTG-CTTCTGCT-CAGAT
* * * * *
8408 GTTCGTAATACATTTGACAACACATTCATCCTTTCATGTGGTT-TTCACACCGAT
1 GTTCGTAAAACATTTGACAACACATTCATCATTTCATGTGCTTCTGCTCA--GAT
* * *
8462 GTTAGTAAAACATTTGACAACACATTCATCCTTTCCTGTGTCTTCTG-TACAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCATTTCATGTG-CTTCTGCT-CAGAT
* * * * * *
8516 GTTCGTAATACATTTGACAACAGATTTATCCTTTCATGTGGCTTCTTCACAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCATTTCATGT-GCTTCTGCTCAGAT
8570 GTT
1 GTT
8573 TGCCAGTGAA
Statistics
Matches: 231, Mismatches: 30, Indels: 22
0.82 0.11 0.08
Matches are distributed among these distances:
52 5 0.02
53 53 0.23
54 167 0.72
55 3 0.01
56 3 0.01
ACGTcount: A:0.28, C:0.22, G:0.13, T:0.38
Consensus pattern (53 bp):
GTTCGTAAAACATTTGACAACACATTCATCATTTCATGTGCTTCTGCTCAGAT
Found at i:8571 original size:108 final size:107
Alignment explanation
Indices: 8252--8572 Score: 459
Period size: 108 Copynumber: 3.0 Consensus size: 107
8242 CACTGGTTCA
* * *
8252 TAAAACATTTGGCAACACATTCATCATTTCCTAT-TGCTTCTGCT-CAGATGTTCGTAAAACATT
1 TAAAACATTTGACAACACATTCATCATTTCCTGTGT-CTTCTG-TACAGATGTTCGTAATACATT
* * * **
8315 TGACAACACATTCATCATTTCATGTGTTTCTACACAGATGTTCT
64 TGACAACACATTCATCCTTTCATGTGGTTCTTCACAGATGTTAG
* *
8359 TCAAACATTTGACAACACATTCATCATTTCATGTGTCTTCTGTACAGATGTTCGTAATACATTTG
1 TAAAACATTTGACAACACATTCATCATTTCCTGTGTCTTCTGTACAGATGTTCGTAATACATTTG
8424 ACAACACATTCATCCTTTCATGTGGTT-TTCACACCGATGTTAG
66 ACAACACATTCATCCTTTCATGTGGTTCTTCACA--GATGTTAG
*
8467 TAAAACATTTGACAACACATTCATCCTTTCCTGTGTCTTCTGTACAGATGTTCGTAATACATTTG
1 TAAAACATTTGACAACACATTCATCATTTCCTGTGTCTTCTGTACAGATGTTCGTAATACATTTG
* *
8532 ACAACAGATTTATCCTTTCATGTGGCTTCTTCACAGATGTT
66 ACAACACATTCATCCTTTCATGTGG-TTCTTCACAGATGTT
8573 TGCCAGTGAA
Statistics
Matches: 193, Mismatches: 15, Indels: 11
0.88 0.07 0.05
Matches are distributed among these distances:
106 6 0.03
107 81 0.42
108 98 0.51
109 2 0.01
110 6 0.03
ACGTcount: A:0.28, C:0.22, G:0.12, T:0.38
Consensus pattern (107 bp):
TAAAACATTTGACAACACATTCATCATTTCCTGTGTCTTCTGTACAGATGTTCGTAATACATTTG
ACAACACATTCATCCTTTCATGTGGTTCTTCACAGATGTTAG
Found at i:12257 original size:2 final size:2
Alignment explanation
Indices: 12250--12292 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
12240 ACAAGGGATG
12250 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
12292 T
1 T
12293 TTGAAAGGAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:13943 original size:36 final size:36
Alignment explanation
Indices: 13903--13980 Score: 111
Period size: 36 Copynumber: 2.2 Consensus size: 36
13893 AGTTTGAAAC
** * *
13903 AAAATGTAATTATGCAAAGATGCAAATACAACAATG
1 AAAATGTAAAAATGCAAAGATGCAAATACAAAAATA
*
13939 AAAATGTAAAAATGCAAAGATGCAAATGCAAAAATA
1 AAAATGTAAAAATGCAAAGATGCAAATACAAAAATA
13975 AAAATG
1 AAAATG
13981 CAAATTGTGC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.58, C:0.09, G:0.14, T:0.19
Consensus pattern (36 bp):
AAAATGTAAAAATGCAAAGATGCAAATACAAAAATA
Found at i:13965 original size:14 final size:14
Alignment explanation
Indices: 13945--13984 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
13935 AATGAAAATG
*
13945 TAAAAATGCAAAGA
1 TAAAAATGCAAAAA
**
13959 TGCAAATGCAAAAA
1 TAAAAATGCAAAAA
13973 TAAAAATGCAAA
1 TAAAAATGCAAA
13985 TTGTGCAATA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.62, C:0.10, G:0.12, T:0.15
Consensus pattern (14 bp):
TAAAAATGCAAAAA
Found at i:13998 original size:28 final size:28
Alignment explanation
Indices: 13945--14046 Score: 77
Period size: 28 Copynumber: 3.7 Consensus size: 28
13935 AATGAAAATG
*
13945 TAAAAATGCAAAGATGCAAATGCAAAAA
1 TAAAAATGCAAAGATGCAAATACAAAAA
*
13973 TAAAAATGCAAATTG-TGC-AATACAAAAG
1 TAAAAATGCAAA--GATGCAAATACAAAAA
* * * * **
14001 CAAACAT-AAAAG-TTCAAATGTAAAAA
1 TAAAAATGCAAAGATGCAAATACAAAAA
*
14027 TGAAAATGCAAAGATGCAAA
1 TAAAAATGCAAAGATGCAAA
14047 ATGCAAATGC
Statistics
Matches: 55, Mismatches: 14, Indels: 10
0.70 0.18 0.13
Matches are distributed among these distances:
25 3 0.05
26 11 0.20
27 7 0.13
28 30 0.55
29 3 0.05
30 1 0.02
ACGTcount: A:0.58, C:0.11, G:0.14, T:0.18
Consensus pattern (28 bp):
TAAAAATGCAAAGATGCAAATACAAAAA
Found at i:14033 original size:14 final size:15
Alignment explanation
Indices: 14016--14053 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
14006 ATAAAAGTTC
*
14016 AAATGTAAAAATG-A
1 AAATGCAAAAATGCA
*
14030 AAATGCAAAGATGCA
1 AAATGCAAAAATGCA
14045 AAATGCAAA
1 AAATGCAAA
14054 TGCATGTATG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 11 0.52
15 10 0.48
ACGTcount: A:0.61, C:0.08, G:0.16, T:0.16
Consensus pattern (15 bp):
AAATGCAAAAATGCA
Found at i:17602 original size:29 final size:28
Alignment explanation
Indices: 17526--17602 Score: 75
Period size: 30 Copynumber: 2.6 Consensus size: 28
17516 CTATAGTATT
* *
17526 AAAATACATAATATATAAATTAATAGACA
1 AAAATA-AAAATATAAAAATTAATAGACA
*
17555 AAAATGAAAAATATTAAAAATTCAGTA-ACA
1 AAAAT-AAAAATA-TAAAAATT-AATAGACA
17585 AAAATATAAAATATAAAA
1 AAAATA-AAAATATAAAA
17603 CCTAAAGATC
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
29 16 0.39
30 22 0.54
31 3 0.07
ACGTcount: A:0.66, C:0.05, G:0.04, T:0.25
Consensus pattern (28 bp):
AAAATAAAAATATAAAAATTAATAGACA
Found at i:18711 original size:3 final size:3
Alignment explanation
Indices: 18703--18758 Score: 69
Period size: 3 Copynumber: 19.0 Consensus size: 3
18693 AATTATTTAT
* * * *
18703 TAA TAA TAA TAA TAA TAA -AA TAA TTA TAA TGA TAA TTA TTA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
18750 TAA TAA TAA
1 TAA TAA TAA
18759 AAATTTAATG
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
2 2 0.04
3 44 0.96
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:18745 original size:15 final size:15
Alignment explanation
Indices: 18688--18753 Score: 66
Period size: 15 Copynumber: 4.6 Consensus size: 15
18678 TTTGTAAATA
18688 AATAA-AATTATT-T
1 AATAATAATTATTAT
* * *
18701 ATTAATAATAATAAT
1 AATAATAATTATTAT
*
18716 AATAA-AATAATTAT
1 AATAATAATTATTAT
*
18730 AATGATAATTATTAT
1 AATAATAATTATTAT
18745 AATAATAAT
1 AATAATAAT
18754 AATAAAAATT
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
13 4 0.10
14 17 0.40
15 21 0.50
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.41
Consensus pattern (15 bp):
AATAATAATTATTAT
Found at i:19719 original size:20 final size:20
Alignment explanation
Indices: 19696--19747 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
19686 AACGCGATCC
19696 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
19716 CCAGAATTGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
19736 CCAAAATCGCAA
1 CCAGAATCGCAA
19748 CGCGATTCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.38, C:0.25, G:0.13, T:0.23
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:19897 original size:20 final size:20
Alignment explanation
Indices: 19803--20151 Score: 418
Period size: 20 Copynumber: 17.4 Consensus size: 20
19793 GATTTTCCAT
* ** *
19803 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
19823 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
19843 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
19863 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
19883 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
19903 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
19923 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
19943 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
19963 AACCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
19983 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
20003 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
20023 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
20043 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
20063 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * **
20083 AATCGCAACGAGAATCTATA
1 AATCGCAACGCGTATCCGTA
*
20103 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
20123 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
20143 AATCACAAC
1 AATCGCAAC
20152 ACTGAAATTT
Statistics
Matches: 285, Mismatches: 36, Indels: 16
0.85 0.11 0.05
Matches are distributed among these distances:
19 3 0.01
20 279 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:23351 original size:19 final size:19
Alignment explanation
Indices: 23329--23665 Score: 373
Period size: 19 Copynumber: 19.5 Consensus size: 19
23319 CGGAAAATAC
*
23329 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
23348 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
23362 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
23382 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
23396 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
23415 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
23434 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
23448 AATCGCAATGCGAAATG-A
1 AATCGCAATGCGAAATGAA
23466 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
23485 AATCGCAA--CGACA-G--
1 AATCGCAATGCGAAATGAA
*
23499 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
23518 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
23537 AATCGCAATGCG-AATGAA
1 AATCGCAATGCGAAATGAA
23555 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
23574 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
23588 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
23607 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
23626 AATCGCAA--CG--AT---
1 AATCGCAATGCGAAATGAA
23638 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
23657 AATCGCAAT
1 AATCGCAAT
23666 AAACGCATTG
Statistics
Matches: 273, Mismatches: 10, Indels: 70
0.77 0.03 0.20
Matches are distributed among these distances:
12 8 0.03
14 50 0.18
15 4 0.01
16 18 0.07
17 16 0.06
18 38 0.14
19 126 0.46
20 13 0.05
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:23444 original size:52 final size:52
Alignment explanation
Indices: 23357--23633 Score: 386
Period size: 52 Copynumber: 5.2 Consensus size: 52
23347 AAATCCCAAC
23357 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
23410 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
23462 ATG-AAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* *
23513 ATTAAAATCGCAATGCGAAATGAAAATCGCAATGCGAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG-A-GAGAATCGCAATGCGAA
*
23569 ATGAAAATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAA
23621 ATGAAAATCGCAA
1 ATGAAAATCGCAA
23634 CGATAATCGC
Statistics
Matches: 213, Mismatches: 5, Indels: 13
0.92 0.02 0.06
Matches are distributed among these distances:
51 61 0.29
52 100 0.47
53 17 0.08
54 7 0.03
55 1 0.00
56 27 0.13
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.14
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:23479 original size:70 final size:71
Alignment explanation
Indices: 23396--23633 Score: 355
Period size: 70 Copynumber: 3.4 Consensus size: 71
23386 GCAACGAGAG
*
23396 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
23461 AATG-A
66 AATGAA
* *
23466 AATCGCAATGCGAAATGAAAATCGCAA--CGACA-G--AATCGCAATGCGAAATTAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG-AA--AGAATCGCAA
23526 TGCGAAATGAA
61 TGCGAAATGAA
23537 AATCGCAATGCG-AATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
23601 AATGAA
66 AATGAA
23607 AATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAA
23634 CGATAATCGC
Statistics
Matches: 151, Mismatches: 5, Indels: 23
0.84 0.03 0.13
Matches are distributed among these distances:
65 8 0.05
67 3 0.02
68 5 0.03
70 91 0.60
71 27 0.18
72 6 0.04
73 3 0.02
75 8 0.05
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.15
Consensus pattern (71 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
AATGAA
Found at i:23558 original size:89 final size:88
Alignment explanation
Indices: 23329--23664 Score: 386
Period size: 89 Copynumber: 3.9 Consensus size: 88
23319 CGGAAAATAC
* *
23329 AATCGCAACGCGAAATGAAAATCCCAA--C---ATGAAAATCGCAATGCGGAAATGAAAATCGCA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGC-GAAATG-AAATCGCA
* * * * *
23389 ACGAGAGAATCG-CAATGCGAAATGAA-
64 ATGCGA-AAT-GAAAAT-CGCAACGAAG
*
23415 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAAATCGCAAT
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAATCGCAAT
23475 GCGAAATGAAAATCGCAACGACAG
66 GCGAAATGAAAATCGCAACGA-AG
*
23499 AATCGCAATGCGAAATTAAAATCGCAATGCGAAATGAAAATCGCAATGCG-AATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATG-AAATCGCAA
23563 TGCGAAATGAAAATCGCAACGAAAG
65 TGCGAAATGAAAATCGCAACG-AAG
23588 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--AT--AATCGCAAT
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAATCGCAAT
23647 GCGAAATGAAAATCGCAA
66 GCGAAATGAAAATCGCAA
23665 TAAACGCATT
Statistics
Matches: 228, Mismatches: 11, Indels: 25
0.86 0.04 0.09
Matches are distributed among these distances:
82 7 0.03
83 34 0.15
84 38 0.17
85 6 0.03
86 43 0.19
87 3 0.01
88 5 0.02
89 91 0.40
90 1 0.00
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.14
Consensus pattern (88 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAATCGCAAT
GCGAAATGAAAATCGCAACGAAG
Found at i:23777 original size:19 final size:19
Alignment explanation
Indices: 23669--23769 Score: 142
Period size: 19 Copynumber: 5.6 Consensus size: 19
23659 TCGCAATAAA
23669 CGCATTGCGA-TTTCATTT
1 CGCATTGCGATTTTCATTT
23687 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
23707 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
23723 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
23740 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
23759 CGCATTGCGAT
1 CGCATTGCGAT
23770 AGTCATTTTT
Statistics
Matches: 74, Mismatches: 2, Indels: 12
0.84 0.02 0.14
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 46 0.62
20 8 0.11
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:23894 original size:14 final size:14
Alignment explanation
Indices: 23875--23911 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
23865 CATCAATTAC
23875 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
23889 ACAAATCATCTTTT
1 ACAAATCAACTTTT
23903 ACAAATCAA
1 ACAAATCAA
23912 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:25333 original size:21 final size:20
Alignment explanation
Indices: 25303--25363 Score: 68
Period size: 21 Copynumber: 3.0 Consensus size: 20
25293 GTGAATCGGG
25303 CTCTTGAATGGTGGGAGGGAC
1 CTCTTGAATGGTGGGAGGG-C
* * **
25324 CTCTTCAATGATGACAGTGGC
1 CTCTTGAATGGTGGGAG-GGC
25345 CTCTTGAATGGTGGGAGGG
1 CTCTTGAATGGTGGGAGGG
25364 GACTCTCGAG
Statistics
Matches: 31, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
20 2 0.06
21 27 0.87
22 2 0.06
ACGTcount: A:0.20, C:0.16, G:0.38, T:0.26
Consensus pattern (20 bp):
CTCTTGAATGGTGGGAGGGC
Found at i:25862 original size:19 final size:19
Alignment explanation
Indices: 25822--25886 Score: 87
Period size: 18 Copynumber: 3.4 Consensus size: 19
25812 TAGTTTACTT
*
25822 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-TAAAA
*
25842 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACTAAAA
*
25861 TCGCAACGCG-AATTAAAA
1 TCGCAACGCGAAACTAAAA
25879 TCGCAACG
1 TCGCAACG
25887 ACAGAATCGC
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
18 14 0.34
19 14 0.34
20 13 0.32
ACGTcount: A:0.45, C:0.28, G:0.15, T:0.12
Consensus pattern (19 bp):
TCGCAACGCGAAACTAAAA
Found at i:25896 original size:14 final size:14
Alignment explanation
Indices: 25877--25933 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
25867 CGCGAATTAA
*
25877 AATCGCAACGACAG
1 AATCGCAACGAAAG
25891 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
25908 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
25924 AATCGCAACG
1 AATCGCAACG
25934 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:25915 original size:19 final size:19
Alignment explanation
Indices: 25822--25955 Score: 110
Period size: 19 Copynumber: 7.6 Consensus size: 19
25812 TAGTTTACTT
* *
25822 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
25842 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
*
25861 TCGCAACGCG-AATTAAAA
1 TCGCAACGCGAAATGAAAA
*
25879 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
25893 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
25912 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
25926 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
25945 TCGCAATGCGA
1 TCGCAACGCGA
25956 TTTTGGTTTC
Statistics
Matches: 94, Mismatches: 9, Indels: 23
0.75 0.07 0.18
Matches are distributed among these distances:
14 16 0.17
16 12 0.13
17 8 0.09
18 12 0.13
19 34 0.36
20 12 0.13
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.12
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:25917 original size:33 final size:33
Alignment explanation
Indices: 25859--25950 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
25849 GCGAAACCAA
* *
25859 AATCGCAACGCG-AATTAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
25891 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
25924 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
25951 TGCGATTTTG
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
32 11 0.20
33 44 0.80
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.12
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:25973 original size:19 final size:19
Alignment explanation
Indices: 25951--26079 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
25941 AAAATCGCAA
25951 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
25970 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
25984 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
26003 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
26017 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
26036 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
26055 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
26075 TGCGA
1 TGCGA
26080 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:25993 original size:33 final size:33
Alignment explanation
Indices: 25951--26042 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
25941 AAAATCGCAA
25951 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
25984 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
26017 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
26043 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:26280 original size:92 final size:93
Alignment explanation
Indices: 26123--26680 Score: 1063
Period size: 92 Copynumber: 6.1 Consensus size: 93
26113 TTGAATGGAT
*
26123 AAATTTACTTTCAACCAAAAGACAAAACAAAGAC-AATACTATTTCACAGCGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
26187 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
26215 AAATTTACTTTCAACC-AAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
26279 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
26307 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
26372 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
26400 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
26464 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
26492 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
26556 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
26584 AAATTTACTTTCAACCAAAAGACAAAACAAAGA-AAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
26648 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
26676 AAATT
1 AAATT
26681 ACTAAGCAAT
Statistics
Matches: 461, Mismatches: 2, Indels: 6
0.98 0.00 0.01
Matches are distributed among these distances:
91 22 0.05
92 324 0.70
93 115 0.25
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:28406 original size:14 final size:14
Alignment explanation
Indices: 28387--28476 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
28377 TTGAAATGAA
28387 AATCGCAACGAGAG
1 AATCGCAACGAGAG
28401 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
28418 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
28434 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
28453 AATCGCAACGAGAG
1 AATCGCAACGAGAG
28467 AATCGCAACG
1 AATCGCAACG
28477 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:28424 original size:33 final size:33
Alignment explanation
Indices: 28379--28493 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
28369 TCTTTTGGTT
28379 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
28412 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
28445 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
28478 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
28494 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:28425 original size:19 final size:18
Alignment explanation
Indices: 28386--28498 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
28376 GTTGAAATGA
28386 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
28401 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
28418 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
28434 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
28451 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
28467 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
28484 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
28499 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:28532 original size:31 final size:33
Alignment explanation
Indices: 28494--28562 Score: 106
Period size: 31 Copynumber: 2.2 Consensus size: 33
28484 AAAATCGCAA
**
28494 TGCGATTTTGGTTTCGCGTTGCGA-T-TCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
28525 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
28558 TGCGA
1 TGCGA
28563 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
31 22 0.65
32 1 0.03
33 11 0.32
ACGTcount: A:0.09, C:0.22, G:0.26, T:0.43
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:28724 original size:33 final size:33
Alignment explanation
Indices: 28682--28752 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
28672 AATACTAACT
*
28682 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
28715 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
28748 TGAAA
1 TGAAA
28753 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:28984 original size:22 final size:22
Alignment explanation
Indices: 28932--28986 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
28922 TGGTTGTGAG
**
28932 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
28954 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
28976 GGATTTCTTCG
1 GGATTTCTTCG
28987 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:29156 original size:20 final size:20
Alignment explanation
Indices: 29131--29323 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
29121 CTTTAAATAT
29131 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
29151 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
29173 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
29192 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
29212 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
29232 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
29252 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
29272 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
29292 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
29312 CGCGTTGCGATT
1 CGCGTTGCGATT
29324 ATGGAAAATC
Statistics
Matches: 146, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 127 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:29318 original size:60 final size:60
Alignment explanation
Indices: 29131--29323 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
29121 CTTTAAATAT
**
29131 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
29192 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
29252 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
29312 CGCGTTGCGATT
1 CGCGTTGCGATT
29324 ATGGAAAATC
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 83 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:29376 original size:21 final size:20
Alignment explanation
Indices: 29291--29388 Score: 79
Period size: 21 Copynumber: 4.8 Consensus size: 20
29281 ATTTATGTGT
* *
29291 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCAAAA
**
29311 TCGCGTTGCGATTATGGAAAA
1 TCGCGTTGCGATT-TTCAAAA
** * **
29332 TCGCAATGCGAATTTCTACTA
1 TCGCGTTGCGATTTTC-AAAA
*
29353 TCGCATTGCGATTTTCAAGAA
1 TCGCGTTGCGATTTTCAA-AA
29374 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
29389 GGAAACTGAT
Statistics
Matches: 59, Mismatches: 16, Indels: 5
0.74 0.20 0.06
Matches are distributed among these distances:
20 15 0.25
21 44 0.75
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.37
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCAAAA
Found at i:29384 original size:42 final size:41
Alignment explanation
Indices: 29291--29384 Score: 93
Period size: 42 Copynumber: 2.3 Consensus size: 41
29281 ATTTATGTGT
* * *
29291 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTATGGAAAA
1 TCGCGTTGCGAATTTCATATTCGCATTGCGATTATGCAAAA
** *
29332 TCGCAATGCGAATTTC-TACTATCGCATTGCGATT-TTCAAGAA
1 TCGCGTTGCGAATTTCATA-T-TCGCATTGCGATTATGCAA-AA
29374 TCGCGTTGCGA
1 TCGCGTTGCGA
29385 TTTTGGAAAC
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
40 2 0.05
41 17 0.40
42 23 0.55
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.34
Consensus pattern (41 bp):
TCGCGTTGCGAATTTCATATTCGCATTGCGATTATGCAAAA
Found at i:29404 original size:20 final size:20
Alignment explanation
Indices: 29379--29428 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
29369 AAGAATCGCG
*
29379 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
29399 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
29419 TTGCGATTCT
1 TTGCGATTCT
29429 AGGGATCGCG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.22, C:0.14, G:0.24, T:0.40
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:29885 original size:63 final size:62
Alignment explanation
Indices: 29756--29885 Score: 201
Period size: 62 Copynumber: 2.1 Consensus size: 62
29746 TATATTTGAT
* *
29756 TTTAATTTTAATATTAGTTTTTAATAAATTAAATATTATTTTTTAATATTATATTATAGATA
1 TTTAATATTAATATTAGTTTTTAATAAATTAAATATTATTTTTTAATATAATATTATAGATA
*
29818 -TTAATATTAATATTAATTTTTTAAATAAATTAAATATTA-TTTTTAATATAATATTATAGATA
1 TTTAATATTAATATT-AGTTTTT-AATAAATTAAATATTATTTTTTAATATAATATTATAGATA
29880 TTTAAT
1 TTTAAT
29886 TTATATCATA
Statistics
Matches: 62, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
61 13 0.21
62 28 0.45
63 21 0.34
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (62 bp):
TTTAATATTAATATTAGTTTTTAATAAATTAAATATTATTTTTTAATATAATATTATAGATA
Found at i:30442 original size:31 final size:31
Alignment explanation
Indices: 30405--30464 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
30395 TAGTTGTATG
* *
30405 AATTATTTAAATTTCAGTATTGTAAAACTAA
1 AATTATTTAAATCTCAGTATTGCAAAACTAA
30436 AATTATTTAAATCTCAGTATTGCAAAACT
1 AATTATTTAAATCTCAGTATTGCAAAACT
30465 CTTTTAAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.40
Consensus pattern (31 bp):
AATTATTTAAATCTCAGTATTGCAAAACTAA
Found at i:32304 original size:6 final size:6
Alignment explanation
Indices: 32295--32319 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
32285 GGGATGATAA
32295 ACGGGG ACGGGG ACGGGG ACGGGG A
1 ACGGGG ACGGGG ACGGGG ACGGGG A
32320 AAACTTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.20, C:0.16, G:0.64, T:0.00
Consensus pattern (6 bp):
ACGGGG
Found at i:32509 original size:12 final size:12
Alignment explanation
Indices: 32485--32530 Score: 76
Period size: 12 Copynumber: 3.9 Consensus size: 12
32475 CGATTCCTTG
32485 CCCAATA-CCGA
1 CCCAATACCCGA
32496 CCCAATACCCGA
1 CCCAATACCCGA
32508 CCCAATACCCGA
1 CCCAATACCCGA
*
32520 CCCATTACCCG
1 CCCAATACCCG
32531 TTTAAATAAC
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
11 7 0.21
12 26 0.79
ACGTcount: A:0.30, C:0.50, G:0.09, T:0.11
Consensus pattern (12 bp):
CCCAATACCCGA
Found at i:37022 original size:14 final size:14
Alignment explanation
Indices: 37003--37030 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
36993 AAGTGAAAGA
37003 ATAGTTATATAATT
1 ATAGTTATATAATT
37017 ATAGTTATATAATT
1 ATAGTTATATAATT
37031 TTGTTATGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
ATAGTTATATAATT
Found at i:39828 original size:18 final size:18
Alignment explanation
Indices: 39805--39839 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
39795 AATAAGTAAC
39805 AATATTATAAATTAAAAA
1 AATATTATAAATTAAAAA
*
39823 AATATTTTAAATTAAAA
1 AATATTATAAATTAAAA
39840 TAAAACGATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
AATATTATAAATTAAAAA
Found at i:40424 original size:34 final size:34
Alignment explanation
Indices: 40386--40450 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
40376 GGACGTTTGG
* *
40386 TTTAC-GGAATGTAAGATTACCTTTGGGAATAACA
1 TTTACTGGAATGTAACATTA-CTATGGGAATAACA
40420 TTTACTGGAATGTAACATTACTATGGGAATA
1 TTTACTGGAATGTAACATTACTATGGGAATA
40451 TTGTATTACC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 15 0.54
35 13 0.46
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.34
Consensus pattern (34 bp):
TTTACTGGAATGTAACATTACTATGGGAATAACA
Found at i:50970 original size:21 final size:20
Alignment explanation
Indices: 50946--50984 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
50936 TATCGACCTG
50946 TTATAAAATAATTAATAAATT
1 TTATAAAATAATT-ATAAATT
* *
50967 TTATCAAATTATTATAAA
1 TTATAAAATAATTATAAA
50985 ATGATGATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (20 bp):
TTATAAAATAATTATAAATT
Found at i:53479 original size:2 final size:2
Alignment explanation
Indices: 53474--53528 Score: 103
Period size: 2 Copynumber: 28.0 Consensus size: 2
53464 TAAATCCATG
53474 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
53516 AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT
53529 GTACAGCAAT
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 51 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:65415 original size:2 final size:2
Alignment explanation
Indices: 65408--65456 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
65398 TTATACATAC
65408 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
65450 AT AT AT A
1 AT AT AT A
65457 ATTTAGTAGA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:65567 original size:16 final size:17
Alignment explanation
Indices: 65543--65575 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
65533 CGTATATTTG
65543 ATCCGAAAA-TTCAGAT
1 ATCCGAAAATTTCAGAT
*
65559 ATCCTAAAATTTCAGAT
1 ATCCGAAAATTTCAGAT
65576 GTGCATGGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.42, C:0.18, G:0.09, T:0.30
Consensus pattern (17 bp):
ATCCGAAAATTTCAGAT
Found at i:73827 original size:137 final size:137
Alignment explanation
Indices: 73581--73841 Score: 425
Period size: 137 Copynumber: 1.9 Consensus size: 137
73571 ACAGAACATG
* *
73581 ATCAGCAAGATACAGAAAAACTGTAAAATATAACTCATTGTTTCCCTAGCCATCCATATAGTTCG
1 ATCAGCAAGATACAGAAAAACTGTAAAATATAACGCATTGTTTCCCTAGCCATACATATAGTTCG
* * **
73646 TTACCCCAATTAAGGAAACGCAGTAAAAGGCCCAATAATCAACATCCAATGCTCGAGAACAAACA
66 TTAACCCAATTAAGGAAACACAAAAAAAGGCCCAATAATCAACATCCAATGCTCGAGAACAAACA
73711 CATGCAT
131 CATGCAT
*
73718 ATCAGCAAGATACAGAAAAACTGTAAAACT-TAACGCATTGTTTCCCTAGCCATACGTATAGTTC
1 ATCAGCAAGATACAGAAAAACTGTAAAA-TATAACGCATTGTTTCCCTAGCCATACATATAGTTC
* *
73782 GTTAACCCGATTATGGAAACACAAAAAAAGGCCCAATAATCAACATCCAATGCTCGAGAA
65 GTTAACCCAATTAAGGAAACACAAAAAAAGGCCCAATAATCAACATCCAATGCTCGAGAA
73842 TGAATACATA
Statistics
Matches: 114, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
137 113 0.99
138 1 0.01
ACGTcount: A:0.41, C:0.23, G:0.14, T:0.22
Consensus pattern (137 bp):
ATCAGCAAGATACAGAAAAACTGTAAAATATAACGCATTGTTTCCCTAGCCATACATATAGTTCG
TTAACCCAATTAAGGAAACACAAAAAAAGGCCCAATAATCAACATCCAATGCTCGAGAACAAACA
CATGCAT
Found at i:78163 original size:2 final size:2
Alignment explanation
Indices: 78156--78199 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
78146 ATTTATAATC
78156 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
78198 TA
1 TA
78200 AAGTTTATTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.