Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001420.1 Hibiscus syriacus cultivar Beakdansim tig00002758_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: 77818
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Found at i:164 original size:2 final size:2
Alignment explanation
Indices: 157--196 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
147 ATTTTCTGAC
157 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
197 AGTTAAAGTA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8362 original size:18 final size:18
Alignment explanation
Indices: 8339--8385 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
8329 ATGTAAAAAT
8339 GGTACTGATACCCAAAGG
1 GGTACTGATACCCAAAGG
8357 GGTACTGATACCCAAAGG
1 GGTACTGATACCCAAAGG
*
8375 GGTACCGATAC
1 GGTACTGATAC
8386 TACTTTACAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.32, C:0.23, G:0.28, T:0.17
Consensus pattern (18 bp):
GGTACTGATACCCAAAGG
Found at i:8562 original size:20 final size:21
Alignment explanation
Indices: 8529--8568 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
8519 GTAGAGAAAA
8529 CATCCCCAAACGGCTATAAAT
1 CATCCCCAAACGGCTATAAAT
8550 CATCCCC-AACGGCTATAAA
1 CATCCCCAAACGGCTATAAA
8569 CGACTACAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.38, C:0.35, G:0.10, T:0.17
Consensus pattern (21 bp):
CATCCCCAAACGGCTATAAAT
Found at i:17375 original size:36 final size:36
Alignment explanation
Indices: 17304--17409 Score: 178
Period size: 36 Copynumber: 2.9 Consensus size: 36
17294 TCACCAATTT
*
17304 AGGTTTAATAAGAAATTTGAGTATTTTTTCTTATTAA
1 AGGTTTCATAAGAAATTTGAGTA-TTTTTCTTATTAA
17341 AGGTTTCATAAGAAATTTGAGTATTTTTCTTATTAA
1 AGGTTTCATAAGAAATTTGAGTATTTTTCTTATTAA
*
17377 AGGTTTCATAAGAAATTTGTGTA-TTTTCTTATT
1 AGGTTTCATAAGAAATTTGAGTATTTTTCTTATT
17410 GAAGATTAAT
Statistics
Matches: 67, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
35 10 0.15
36 35 0.52
37 22 0.33
ACGTcount: A:0.32, C:0.05, G:0.14, T:0.49
Consensus pattern (36 bp):
AGGTTTCATAAGAAATTTGAGTATTTTTCTTATTAA
Found at i:23602 original size:34 final size:35
Alignment explanation
Indices: 23564--23634 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
23554 AAGCCTATGA
23564 CTTAACC-TTTTTTATCCCCAGGGAAGAAGAAAAG
1 CTTAACCTTTTTTTATCCCCAGGGAAGAAGAAAAG
23598 CTTAACCTTTTTTTATCCCCAGGGAAGAAGAAAAG
1 CTTAACCTTTTTTTATCCCCAGGGAAGAAGAAAAG
23633 CT
1 CT
23635 CAAAAACGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 7 0.19
35 29 0.81
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (35 bp):
CTTAACCTTTTTTTATCCCCAGGGAAGAAGAAAAG
Found at i:24013 original size:20 final size:20
Alignment explanation
Indices: 23990--24041 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
23980 AACGCGATCC
23990 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
24010 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
24030 CCAAAATCGCAA
1 CCAGAATCGCAA
24042 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:24058 original size:21 final size:20
Alignment explanation
Indices: 24031--24129 Score: 72
Period size: 21 Copynumber: 4.8 Consensus size: 20
24021 AATCAGTTTC
24031 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
24052 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
24073 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
24093 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
24114 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
24130 ACACATAAAT
Statistics
Matches: 59, Mismatches: 17, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
20 16 0.27
21 43 0.73
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:24158 original size:20 final size:20
Alignment explanation
Indices: 24096--24289 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
24086 CGATTTTCCA
* ** *
24096 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
24116 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
24136 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
24156 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
24176 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
24196 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
24216 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
24236 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
24256 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
24277 AAATCGCAACGCG
1 AAATCGCAACGCG
24290 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:24180 original size:60 final size:60
Alignment explanation
Indices: 24096--24289 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
24086 CGATTTTCCA
* ** * *
24096 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
24156 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
24216 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
24277 AAATCGCAACGCG
1 AAATCGCAACGCG
24290 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:24710 original size:33 final size:33
Alignment explanation
Indices: 24671--24741 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
24661 TTCACTTAGA
*
24671 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
24704 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
24737 TTTCA
1 TTTCA
24742 AGTTAGTATT
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:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:24881 original size:14 final size:14
Alignment explanation
Indices: 24862--24916 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
24852 AGAATGACTG
24862 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
24876 TCGCAACGCGAAATGAAAA
1 TCGCAA--CG--A-GAGAA
24895 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
24909 TCGCAACG
1 TCGCAACG
24917 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:24899 original size:33 final size:33
Alignment explanation
Indices: 24862--24932 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
24852 AGAATGACTG
**
24862 TCGCAACGAGAGAATCGCAACGCGAAATGAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
24895 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
24928 TCGCA
1 TCGCA
24933 TTGCGATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:24950 original size:19 final size:19
Alignment explanation
Indices: 24928--25025 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
24918 GAAACCAAAA
*
24928 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
24947 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
24961 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
24980 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
24994 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
25013 TCGCGTTGCGATT
1 TCGCGTTGCGATT
25026 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:24969 original size:14 final size:14
Alignment explanation
Indices: 24950--25039 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
24940 TTTCATTTCG
24950 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
24964 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
24983 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
24997 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
25014 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
25030 CGTTGCGATT
1 CGTTGCGATT
25040 TTCATTTCAA
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:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:24975 original size:33 final size:33
Alignment explanation
Indices: 24933--25047 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
24923 CAAAATCGCA
24933 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
24966 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
24999 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
25032 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
25048 AACCAAAAGA
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:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:26974 original size:185 final size:186
Alignment explanation
Indices: 26744--27125 Score: 748
Period size: 185 Copynumber: 2.1 Consensus size: 186
26734 TAGATTGCTT
26744 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
26809 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
26874 GTGTATTCTTTAACACTGTGAAATA-TATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
26929 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
26994 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
27059 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
27115 AGTAAATTTAT
1 AGTAAATTTAT
27126 CCATTCAAGT
Statistics
Matches: 194, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
185 154 0.79
186 40 0.21
ACGTcount: A:0.23, C:0.13, G:0.19, T:0.46
Consensus pattern (186 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:27058 original size:93 final size:93
Alignment explanation
Indices: 26744--27123 Score: 744
Period size: 93 Copynumber: 4.1 Consensus size: 93
26734 TAGATTGCTT
*
26744 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
26809 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
26837 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
26901 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
26929 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
26994 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
27022 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
27087 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
27115 AGTAAATTT
1 AGTAAATTT
27124 ATCCATTCAA
Statistics
Matches: 285, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
92 92 0.32
93 193 0.68
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:27207 original size:19 final size:19
Alignment explanation
Indices: 27167--27295 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
27157 TAGTTTACTT
* *
27167 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
27187 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
27206 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
27225 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
27239 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
27258 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
27272 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
27291 TCGCA
1 TCGCA
27296 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:27246 original size:33 final size:32
Alignment explanation
Indices: 27203--27295 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
27193 CGCGAAACCA
**
27203 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
27235 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
27268 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
27296 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:27293 original size:52 final size:52
Alignment explanation
Indices: 27167--27295 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
27157 TAGTTTACTT
**
27167 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
27219 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
27272 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
27296 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:27313 original size:19 final size:19
Alignment explanation
Indices: 27291--27425 Score: 137
Period size: 19 Copynumber: 7.6 Consensus size: 19
27281 GAAACCAAAA
*
27291 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
27310 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
27326 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
27343 TCGCGTTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
27359 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
27376 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
27395 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
27415 TCGTGTTGCGA
1 TCGCGTTGCGA
27426 AAGTAAACTA
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:27332 original size:14 final size:14
Alignment explanation
Indices: 27313--27369 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
27303 TTTCATTTCG
27313 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
27327 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
27344 CGCGTTGCGATTCTGT
1 --CGTTGCGATTCTTT
27360 CGTTGCGATT
1 CGTTGCGATT
27370 TTCATTTCGC
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:0.09, C:0.21, G:0.25, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:27338 original size:33 final size:33
Alignment explanation
Indices: 27296--27388 Score: 177
Period size: 33 Copynumber: 2.8 Consensus size: 33
27286 CAAAATCGCA
*
27296 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
27329 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
27362 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
27389 TTGGTTTCGC
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.10, C:0.20, G:0.23, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:29283 original size:38 final size:38
Alignment explanation
Indices: 29240--29312 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
29230 AATTGATTGT
*
29240 TTTTTGATTGTTTAATTGATTTGTAAAAGTTGATTCAA
1 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATTCAA
29278 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATT
1 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATT
29313 TGTAAAAGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.29, C:0.01, G:0.16, T:0.53
Consensus pattern (38 bp):
TTTTTGATTGTTTAATTGATTTGTAAAAGATGATTCAA
Found at i:29299 original size:19 final size:19
Alignment explanation
Indices: 29235--29299 Score: 51
Period size: 19 Copynumber: 3.4 Consensus size: 19
29225 AGTTTAATTG
*
29235 ATTGTTTTTTGATTGTTTA
1 ATTGATTTTTGATTGTTTA
* * ** *
29254 ATTGATTTGTAAAAG-TTG
1 ATTGATTTTTGATTGTTTA
*
29272 ATTCAATTTTTGATTGTTTA
1 ATT-GATTTTTGATTGTTTA
29292 ATTGATTT
1 ATTGATTT
29300 GTAAAAGATG
Statistics
Matches: 31, Mismatches: 13, Indels: 4
0.65 0.27 0.08
Matches are distributed among these distances:
18 5 0.16
19 21 0.68
20 5 0.16
ACGTcount: A:0.25, C:0.02, G:0.15, T:0.58
Consensus pattern (19 bp):
ATTGATTTTTGATTGTTTA
Found at i:29313 original size:14 final size:14
Alignment explanation
Indices: 29294--29329 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
29284 ATTGTTTAAT
29294 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
29308 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
29322 TGATTTGT
1 TGATTTGT
29330 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:29501 original size:19 final size:19
Alignment explanation
Indices: 29456--29896 Score: 564
Period size: 19 Copynumber: 24.7 Consensus size: 19
29446 GAAATGAAAA
29456 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
29475 TCCGCATTGCGATTTTCATT
1 T-CGCATTGCGATTTTCATT
*
29495 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
29511 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
29528 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
29547 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
29566 TCGTATTGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
29585 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
29604 TCGCATTGCGA--TTC---
1 TCGCATTGCGATTTTCATT
*
29618 TCGCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
29637 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
29656 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
29672 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
29689 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
29708 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
29727 TCGTATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
29746 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
29765 TCGCATTGCGA--TTC---
1 TCGCATTGCGATTTTCATT
*
29779 TCGCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
29798 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
29817 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
29833 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
29850 TCCGCATTGCGATTTTCA--
1 T-CGCATTGCGATTTTCATT
*
29868 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
29884 TCGCGTTGCGATT
1 TCGCATTGCGATT
29897 GTATTTTCCG
Statistics
Matches: 372, Mismatches: 18, Indels: 64
0.82 0.04 0.14
Matches are distributed among these distances:
14 49 0.13
16 29 0.08
17 26 0.07
18 3 0.01
19 234 0.63
20 31 0.08
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:29544 original size:52 final size:52
Alignment explanation
Indices: 29461--29868 Score: 663
Period size: 52 Copynumber: 7.6 Consensus size: 52
29451 GAAAATCGCA
29461 TTGCGATTTTCATTTCCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTT-CGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
29514 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* *
29569 TATTGCGATTTTAATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCGCG
1 --TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCG
29623 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
29675 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
*
29730 TATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCGCG
1 --TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCG
29784 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCG
29836 TTGCGATTTTCATTTCCGCATTGCGATTTTCAT
1 TTGCGATTTTCATTT-CGCATTGCGATTTTCAT
29869 GTTGGGATTT
Statistics
Matches: 334, Mismatches: 10, Indels: 22
0.91 0.03 0.06
Matches are distributed among these distances:
52 189 0.57
53 32 0.10
54 12 0.04
55 14 0.04
57 87 0.26
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.47
Consensus pattern (52 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:29653 original size:161 final size:161
Alignment explanation
Indices: 29456--29868 Score: 790
Period size: 161 Copynumber: 2.6 Consensus size: 161
29446 GAAATGAAAA
*
29456 TCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGAT
1 TCGCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGAT
29521 TTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTAATTT
65 TTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTAATTT
29586 CGCATTGCGATTTTCATTTCGCATTGCGATTC
130 CGCATTGCGATTTTCATTTCGCATTGCGATTC
29618 TCGCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATT
1 TCGCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATT
*
29683 TTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTCATTTC
66 TTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTAATTTC
29748 GCATTGCGATTTTCATTTCGCATTGCGATTC
131 GCATTGCGATTTTCATTTCGCATTGCGATTC
29779 TCGCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATT
1 TCGCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATT
29844 TTCATTTCCGCATTGCGATTTTCAT
66 TTCATTT-CGCATTGCGATTTTCAT
29869 GTTGGGATTT
Statistics
Matches: 248, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
161 212 0.85
162 36 0.15
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.46
Consensus pattern (161 bp):
TCGCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATT
TTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTAATTTC
GCATTGCGATTTTCATTTCGCATTGCGATTC
Found at i:32217 original size:12 final size:12
Alignment explanation
Indices: 32200--32224 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
32190 TCTTCGGGGA
32200 CTTTTTCTTCTT
1 CTTTTTCTTCTT
32212 CTTTTTCTTCTT
1 CTTTTTCTTCTT
32224 C
1 C
32225 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:32433 original size:24 final size:24
Alignment explanation
Indices: 32399--32445 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
32389 CTGAAACATC
32399 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
32423 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
32446 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:33147 original size:20 final size:20
Alignment explanation
Indices: 33119--33487 Score: 449
Period size: 20 Copynumber: 18.4 Consensus size: 20
33109 AAATTTCAGT
* * * *
33119 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
* *
33139 GTTGCGATTTTCGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
33159 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
33179 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
33199 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
33219 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
33239 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
33259 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
33279 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
33299 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
33319 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
33339 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
33359 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
33379 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
33399 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
33419 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
33439 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
33459 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
33479 GTTGCGATT
1 GTTGCGATT
33488 ATGGAAAATC
Statistics
Matches: 307, Mismatches: 34, Indels: 16
0.86 0.10 0.04
Matches are distributed among these distances:
19 5 0.02
20 297 0.97
21 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:35742 original size:13 final size:13
Alignment explanation
Indices: 35724--35749 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
35714 TATTTTTATG
35724 TTTTTTTAAAATA
1 TTTTTTTAAAATA
35737 TTTTTTTAAAATA
1 TTTTTTTAAAATA
35750 ATTAAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTTTTTAAAATA
Found at i:40614 original size:29 final size:30
Alignment explanation
Indices: 40558--40623 Score: 73
Period size: 29 Copynumber: 2.2 Consensus size: 30
40548 CTCGAAAAAT
* **
40558 AATTTGGTGTCTAAAGAATTTTTCGTTA-A
1 AATTTAGTGTCTAAAGAATTTTAAGTTATA
40587 AATTTAGTGTCTAAAG-ATTTTAAAGTTATA
1 AATTTAGTGTCTAAAGAATTTT-AAGTTATA
*
40617 CATTTAG
1 AATTTAG
40624 GTGTATGCCG
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
28 5 0.16
29 19 0.61
30 7 0.23
ACGTcount: A:0.35, C:0.06, G:0.15, T:0.44
Consensus pattern (30 bp):
AATTTAGTGTCTAAAGAATTTTAAGTTATA
Found at i:42896 original size:108 final size:108
Alignment explanation
Indices: 42727--42932 Score: 331
Period size: 108 Copynumber: 1.9 Consensus size: 108
42717 CTCTATTTAA
* * * * *
42727 GGGTCTGGTCTGGCTTAACTCTTGATATAGTCCCTTGGTTTCGAGTGGAAAGGAGCTCGATGCTC
1 GGGTCTGGCCTGGCTTAACTCTTGATATAGTCCCCTGGTTTCAAGTGGAAAGAAGCACGATGCTC
* * *
42792 TGTCTTGGTTTCGAGTCTTGCGGATGAAGAAATAGTTACTTAG
66 CGTCTTGGTTTCGAGTCATACGGATGAAGAAATAGTTACTTAG
42835 GGGTCTGGCCTGGCTTAACTCTTGATATAGTCCCCTGGTTTCAAGTGGAAAGAAGCACGATGCTC
1 GGGTCTGGCCTGGCTTAACTCTTGATATAGTCCCCTGGTTTCAAGTGGAAAGAAGCACGATGCTC
*
42900 CGTCTTGGTTTCGAGTCATATGGATGAAGAAAT
66 CGTCTTGGTTTCGAGTCATACGGATGAAGAAAT
42933 GACATTGGGA
Statistics
Matches: 89, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
108 89 1.00
ACGTcount: A:0.21, C:0.18, G:0.29, T:0.32
Consensus pattern (108 bp):
GGGTCTGGCCTGGCTTAACTCTTGATATAGTCCCCTGGTTTCAAGTGGAAAGAAGCACGATGCTC
CGTCTTGGTTTCGAGTCATACGGATGAAGAAATAGTTACTTAG
Found at i:43690 original size:3 final size:3
Alignment explanation
Indices: 43682--43706 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
43672 AAGTTGAATG
43682 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
43707 CAACAACAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:44278 original size:29 final size:28
Alignment explanation
Indices: 44208--44278 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 28
44198 TAATATTTTA
*
44208 ATAATATTATTATTTGAATAAATAATAAT
1 ATAAT-TTATCATTTGAATAAATAATAAT
* *
44237 ATATTATTT-TCATTTTAATAATTAATTAAT
1 ATA--ATTTATCATTTGAATAAATAA-TAAT
44267 ATAATTTATCAT
1 ATAATTTATCAT
44279 ATTTTTCATA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
28 4 0.11
29 20 0.57
30 9 0.26
31 2 0.06
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (28 bp):
ATAATTTATCATTTGAATAAATAATAAT
Found at i:44403 original size:27 final size:29
Alignment explanation
Indices: 44370--44445 Score: 77
Period size: 27 Copynumber: 2.7 Consensus size: 29
44360 TAATATAAAG
44370 TATTTTAATATTTAAA-AATATTATT-AT
1 TATTTTAATATTTAAATAATATTATTCAT
* *
44397 TATTTTATTA-ATAAATAATATTATTCAT
1 TATTTTAATATTTAAATAATATTATTCAT
* *
44425 TTTATTTGATATTTATAATAA
1 TAT-TTTAATATTTA-AATAA
44446 AGAACTTTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
26 4 0.11
27 18 0.47
28 4 0.11
29 5 0.13
30 2 0.05
31 5 0.13
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (29 bp):
TATTTTAATATTTAAATAATATTATTCAT
Found at i:44405 original size:24 final size:26
Alignment explanation
Indices: 44378--44431 Score: 78
Period size: 24 Copynumber: 2.2 Consensus size: 26
44368 AGTATTTTAA
*
44378 TATTTAA-AAATATTATTATT-ATTT
1 TATTTAATAAATAATATTATTCATTT
44402 TA-TTAATAAATAATATTATTCATTT
1 TATTTAATAAATAATATTATTCATTT
44427 TATTT
1 TATTT
44432 GATATTTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 4 0.15
24 14 0.54
25 6 0.23
26 2 0.08
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (26 bp):
TATTTAATAAATAATATTATTCATTT
Found at i:47552 original size:23 final size:23
Alignment explanation
Indices: 47526--47569 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
47516 GTTAATTAGA
*
47526 AAATAGTTAAAATTA-TTATTTTT
1 AAATAG-TAAAATAATTTATTTTT
47549 AAATAGTAAAATAATTTATTT
1 AAATAGTAAAATAATTTATTT
47570 AATATTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (23 bp):
AAATAGTAAAATAATTTATTTTT
Found at i:47581 original size:14 final size:15
Alignment explanation
Indices: 47562--47591 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
47552 TAGTAAAATA
47562 ATTTATTT-AATATT
1 ATTTATTTCAATATT
47576 ATTTATTTCAATATT
1 ATTTATTTCAATATT
47591 A
1 A
47592 ATATTAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (15 bp):
ATTTATTTCAATATT
Found at i:54531 original size:14 final size:14
Alignment explanation
Indices: 54512--54541 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
54502 TATTTATTTA
*
54512 TTTTAAATATATAT
1 TTTTAAAAATATAT
54526 TTTTAAAAATATAT
1 TTTTAAAAATATAT
54540 TT
1 TT
54542 AAAGTTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTTAAAAATATAT
Found at i:55278 original size:18 final size:18
Alignment explanation
Indices: 55236--55288 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 18
55226 TAAAAAATGG
55236 GTGATCTTTTTTTTAGTA
1 GTGATCTTTTTTTTAGTA
55254 -TG-T-TTTTTATTT-GTA
1 GTGATCTTTTT-TTTAGTA
55269 GTGATCTTTTCTTTTTAGTA
1 GTGATC-TTT-TTTTTAGTA
55289 TGGTTTTGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 12
0.70 0.00 0.30
Matches are distributed among these distances:
15 8 0.29
16 6 0.21
17 3 0.11
19 6 0.21
20 5 0.18
ACGTcount: A:0.15, C:0.06, G:0.15, T:0.64
Consensus pattern (18 bp):
GTGATCTTTTTTTTAGTA
Found at i:55290 original size:35 final size:33
Alignment explanation
Indices: 55236--55304 Score: 102
Period size: 35 Copynumber: 2.0 Consensus size: 33
55226 TAAAAAATGG
* *
55236 GTGATCTTTTTTTTAGTATGTTTTTTATTTGTA
1 GTGATCTTTTTTTTAGTATGGTTTTGATTTGTA
55269 GTGATCTTTTCTTTTTAGTATGGTTTTGATTTGTA
1 GTGATC-TTT-TTTTTAGTATGGTTTTGATTTGTA
55304 G
1 G
55305 CTTTGATGTG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 6 0.19
34 3 0.09
35 23 0.72
ACGTcount: A:0.14, C:0.04, G:0.19, T:0.62
Consensus pattern (33 bp):
GTGATCTTTTTTTTAGTATGGTTTTGATTTGTA
Found at i:55353 original size:25 final size:24
Alignment explanation
Indices: 55325--55381 Score: 96
Period size: 24 Copynumber: 2.4 Consensus size: 24
55315 TAACCATTAC
55325 GGGGGTCCTCTGCTGTAATTCGTA
1 GGGGGTCCTCTGCTGTAATTCGTA
*
55349 AGGGGTCCTCTGCTGTAATTCGTA
1 GGGGGTCCTCTGCTGTAATTCGTA
*
55373 GAGGGTCCT
1 GGGGGTCCT
55382 TTTTGAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.14, C:0.21, G:0.33, T:0.32
Consensus pattern (24 bp):
GGGGGTCCTCTGCTGTAATTCGTA
Found at i:62838 original size:121 final size:121
Alignment explanation
Indices: 62665--62905 Score: 365
Period size: 121 Copynumber: 2.0 Consensus size: 121
62655 TATTTTTTTT
* * * * *
62665 ACCAAATTTGAGACACATGCTCCTAAACCATAGTAGAATACATGTGTGCTTTCAATTCCTCTTTT
1 ACCAAATTTGAGACAAAAGCTCCTAAACCATAGTAGAATACACGTGTACTTTCAATTCCTATTTT
* * * * *
62730 TTATTACAATTTTTTTATTTTTCACTTTAATCCTTGAATTTGTCATAATCTCCTTC
66 TGATAACAAATTTTTTATTTTTCAATTTAATCCTTGAATTTGTCATAAGCTCCTTC
*
62786 ACCAAATTTGAGCCAAAAGCTCCTAAACCATAGTAGAATACACGTGTACTTTCAATTCCTATTTT
1 ACCAAATTTGAGACAAAAGCTCCTAAACCATAGTAGAATACACGTGTACTTTCAATTCCTATTTT
* *
62851 TGATAACAAATTTTTTATTTTTCAATTTAATCCTTTAATTTTTCATAAGCTCCTT
66 TGATAACAAATTTTTTATTTTTCAATTTAATCCTTGAATTTGTCATAAGCTCCTT
62906 ATTCCTTCAA
Statistics
Matches: 107, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
121 107 1.00
ACGTcount: A:0.30, C:0.20, G:0.08, T:0.42
Consensus pattern (121 bp):
ACCAAATTTGAGACAAAAGCTCCTAAACCATAGTAGAATACACGTGTACTTTCAATTCCTATTTT
TGATAACAAATTTTTTATTTTTCAATTTAATCCTTGAATTTGTCATAAGCTCCTTC
Found at i:63202 original size:21 final size:20
Alignment explanation
Indices: 63172--63224 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
63162 TCTTTAAAAT
63172 ATAATATTATGAATATATTTG
1 ATAATATTAT-AATATATTTG
* *
63193 ATAATTTTATATTATATTTG
1 ATAATATTATAATATATTTG
63213 AT-ATATTA-AATA
1 ATAATATTATAATA
63225 ACATTATAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
18 3 0.11
19 5 0.18
20 11 0.39
21 9 0.32
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (20 bp):
ATAATATTATAATATATTTG
Found at i:63250 original size:2 final size:2
Alignment explanation
Indices: 63243--63310 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
63233 ATATGAAAGA
63243 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
63285 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
63311 GGTTAGATAA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:72858 original size:17 final size:17
Alignment explanation
Indices: 72824--72871 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
72814 ATCAAGAAAA
* *
72824 ATTATTATTTTAGAGAG
1 ATTATTAATTTATAGAG
*
72841 ATTATTAATTTATCGAG
1 ATTATTAATTTATAGAG
*
72858 AATATTAATTTATA
1 ATTATTAATTTATA
72872 AAGGTTCTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.40, C:0.02, G:0.10, T:0.48
Consensus pattern (17 bp):
ATTATTAATTTATAGAG
Found at i:75116 original size:18 final size:20
Alignment explanation
Indices: 75093--75134 Score: 61
Period size: 18 Copynumber: 2.2 Consensus size: 20
75083 AGGTATTTTA
75093 GTTTAAATAGT-TTTAAG-T
1 GTTTAAATAGTATTTAAGAT
*
75111 GTTTAATTAGTATTTAAGAT
1 GTTTAAATAGTATTTAAGAT
75131 GTTT
1 GTTT
75135 TAGCTTGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 10 0.48
19 6 0.29
20 5 0.24
ACGTcount: A:0.31, C:0.00, G:0.17, T:0.52
Consensus pattern (20 bp):
GTTTAAATAGTATTTAAGAT
Found at i:75146 original size:63 final size:63
Alignment explanation
Indices: 75012--75153 Score: 155
Period size: 63 Copynumber: 2.2 Consensus size: 63
75002 TATTTTATCT
* *
75012 TTGTTTTATGTATTTTAGTTGAAATAAGTTTTAGTGTTTTAATTAGGATTTAGAATATTATAT
1 TTGTTTTAGGTATTTTAGTTGAAATAAGTTTTAGTGTTTTAATTAGGATTTAGAATATTATAC
* * * * *
75075 TATTTTTTAGGTATTTTAGTTTAAAT-AGTTTTAAGTG-TTTAATTAGTATTTA-AGATGTTTTA
1 T-TGTTTTAGGTATTTTAGTTGAAATAAGTTTT-AGTGTTTTAATTAGGATTTAGA-ATATTATA
75137 GC
63 -C
*
75139 TTGTTTTAGGAATTT
1 TTGTTTTAGGTATTT
75154 GAAGGCTATA
Statistics
Matches: 66, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
62 1 0.02
63 39 0.59
64 26 0.39
ACGTcount: A:0.28, C:0.01, G:0.16, T:0.55
Consensus pattern (63 bp):
TTGTTTTAGGTATTTTAGTTGAAATAAGTTTTAGTGTTTTAATTAGGATTTAGAATATTATAC
Found at i:75657 original size:20 final size:20
Alignment explanation
Indices: 75628--75665 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
75618 TTTCAAAGGG
75628 ATGCACCGATGCAACAATCT
1 ATGCACCGATGCAACAATCT
* *
75648 ATGCATCGATGCACCAAT
1 ATGCACCGATGCAACAAT
75666 GAATAAATTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.29, G:0.16, T:0.21
Consensus pattern (20 bp):
ATGCACCGATGCAACAATCT
Found at i:75764 original size:46 final size:44
Alignment explanation
Indices: 75712--75815 Score: 147
Period size: 46 Copynumber: 2.3 Consensus size: 44
75702 TGCACTATCC
* *
75712 ATGCATCGATGCACTCAGGGT-TTTATGAAAACATCGAATGCATTT
1 ATGCATCGATGCACTCAAGCTATTT-TG-AAACATCGAATGCATTT
75757 GATGCATCGATGCACTCAAGCTATTTTGAAACATCGAATGCATTT
1 -ATGCATCGATGCACTCAAGCTATTTTGAAACATCGAATGCATTT
*
75802 ATACATCGATGCAC
1 ATGCATCGATGCAC
75816 CCTTAGTGCA
Statistics
Matches: 54, Mismatches: 3, Indels: 4
0.89 0.05 0.07
Matches are distributed among these distances:
44 13 0.24
45 17 0.31
46 21 0.39
47 3 0.06
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (44 bp):
ATGCATCGATGCACTCAAGCTATTTTGAAACATCGAATGCATTT
Found at i:77032 original size:23 final size:21
Alignment explanation
Indices: 76998--77040 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
76988 CTGGAATTTT
76998 ATGTTCTTTTAAAATCAAGAAAA
1 ATGTTCTTTT-AAATC-AGAAAA
77021 ATGTT-TTATTAAATCAGAAA
1 ATGTTCTT-TTAAATCAGAAA
77041 CACCACAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 5 0.26
22 7 0.37
23 7 0.37
ACGTcount: A:0.47, C:0.07, G:0.09, T:0.37
Consensus pattern (21 bp):
ATGTTCTTTTAAATCAGAAAA
Done.