Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005893.1 Hibiscus syriacus cultivar Beakdansim tig00013834_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: 62287
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1082 original size:14 final size:14
Alignment explanation
Indices: 1063--1090 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1053 CCTGATACCA
1063 TGTAGAAAACAGAC
1 TGTAGAAAACAGAC
1077 TGTAGAAAACAGAC
1 TGTAGAAAACAGAC
1091 AAGTCTGTTA
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:0.50, C:0.14, G:0.21, T:0.14
Consensus pattern (14 bp):
TGTAGAAAACAGAC
Found at i:5001 original size:18 final size:19
Alignment explanation
Indices: 4978--5013 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
4968 ATTCTTTTTT
4978 AAATTTATGA-ATATTATA
1 AAATTTATGATATATTATA
*
4996 AAATTTATTATATATTAT
1 AAATTTATGATATATTAT
5014 TATTATTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (19 bp):
AAATTTATGATATATTATA
Found at i:5035 original size:14 final size:14
Alignment explanation
Indices: 5016--5046 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
5006 TATATTATTA
*
5016 TTATTTTAATTTAT
1 TTATTTGAATTTAT
5030 TTATTTGAATTTAT
1 TTATTTGAATTTAT
5044 TTA
1 TTA
5047 AATATTTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (14 bp):
TTATTTGAATTTAT
Found at i:5996 original size:12 final size:12
Alignment explanation
Indices: 5973--6019 Score: 58
Period size: 12 Copynumber: 3.7 Consensus size: 12
5963 ATTTTTCAAT
5973 TTTAATTTTTTTA
1 TTTAA-TTTTTTA
5986 TTTAATTTTTTA
1 TTTAATTTTTTA
5998 TTTAATTTCATTTA
1 TTTAATTT--TTTA
*
6012 TATAATTT
1 TTTAATTT
6020 GAATTTCATT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
12 15 0.48
13 5 0.16
14 11 0.35
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (12 bp):
TTTAATTTTTTA
Found at i:6000 original size:26 final size:28
Alignment explanation
Indices: 5966--6037 Score: 69
Period size: 26 Copynumber: 2.5 Consensus size: 28
5956 GAGGTACATT
*
5966 TTTCAATTTTAATTTTTTTATTTAATTT-
1 TTTC-ATTTTAATTTTTTTATATAATTTA
*
5994 TTT-A-TTTAATTTCATTTATATAATTTGAA
1 TTTCATTTTAATTT-TTTTATATAATTT--A
6023 TTTCATTTTAATTTT
1 TTTCATTTTAATTTT
6038 GATAAAAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
25 8 0.23
26 12 0.34
28 3 0.09
29 3 0.09
30 1 0.03
31 8 0.23
ACGTcount: A:0.28, C:0.04, G:0.01, T:0.67
Consensus pattern (28 bp):
TTTCATTTTAATTTTTTTATATAATTTA
Found at i:8076 original size:23 final size:23
Alignment explanation
Indices: 8049--8112 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 23
8039 GAGTTGAGGG
**
8049 ATTCTATGTGGTCTTTCGGGAT-A
1 ATTCTATGTGGTCTTTCACG-TCA
* *
8072 ATTCTATGTAGTCCTTCACGTCA
1 ATTCTATGTGGTCTTTCACGTCA
8095 ATTCTATGTGGTCTTTCA
1 ATTCTATGTGGTCTTTCA
8113 GAGACTTTGG
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
22 1 0.03
23 33 0.97
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.44
Consensus pattern (23 bp):
ATTCTATGTGGTCTTTCACGTCA
Found at i:9829 original size:31 final size:32
Alignment explanation
Indices: 9777--9841 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 32
9767 TTTTAGGTGT
*
9777 GTGTATGTGTATGCTTTTATTTACTGTTTTAG
1 GTGTATGTGTATGCTTTTATTTACTGTTTAAG
*
9809 GTGTATGTGTATG-TTTTATTTATTGTTTAAG
1 GTGTATGTGTATGCTTTTATTTACTGTTTAAG
9840 GT
1 GT
9842 TTGTTAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 18 0.58
32 13 0.42
ACGTcount: A:0.17, C:0.03, G:0.23, T:0.57
Consensus pattern (32 bp):
GTGTATGTGTATGCTTTTATTTACTGTTTAAG
Found at i:9941 original size:26 final size:27
Alignment explanation
Indices: 9889--9941 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
9879 GGTATGCTTC
*
9889 ATGTCATGTTTAGTAGTTTGTTGTTTA
1 ATGTAATGTTTAGTAGTTTGTTGTTTA
* *
9916 ATGTAATGTTTA-TGGTTTGTTTTTTA
1 ATGTAATGTTTAGTAGTTTGTTGTTTA
9942 TAGTTCACAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 12 0.52
27 11 0.48
ACGTcount: A:0.19, C:0.02, G:0.21, T:0.58
Consensus pattern (27 bp):
ATGTAATGTTTAGTAGTTTGTTGTTTA
Found at i:10907 original size:82 final size:81
Alignment explanation
Indices: 10811--11074 Score: 291
Period size: 81 Copynumber: 3.2 Consensus size: 81
10801 ATATCATAGT
* * *
10811 GTTTTCTATTATTATTTAGAGAATCTCTGCCATGTCATAGTGTTTCATCCCATCCGAAATGAAAG
1 GTTTTCCATTATTATTCAGAGAATCTCTGACATGTCATAGTGTTTCATCCCATCCGAAATGAAAG
10876 ACGCATTATAGGGAAAC
66 ACGCATTA-AGGGAAAC
* * * * *
10893 ATTTTCCTTTATTATTCAGATAATCTCTTACATGTCATAGTGTTCCATCCCATCCGAAATG-AA-
1 GTTTTCCATTATTATTCAGAGAATCTCTGACATGTCATAGTGTTTCATCCCATCCGAAATGAAAG
* *
10956 ATGCATTCCAGGGGAAAC
66 ACGCATT--AAGGGAAAC
* * * * * * *
10974 GTTTTCCATTATTATTGAAAGGATATATGTCATATCATAGTGTTTCATCCCATCCGAAATGAAAG
1 GTTTTCCATTATTATTCAGAGAATCTCTGACATGTCATAGTGTTTCATCCCATCCGAAATGAAA-
*
11039 GTACG-GTTCAAGGGAAAC
65 G-ACGCATT-AAGGGAAAC
11057 GTTTTCCATTATTATTCA
1 GTTTTCCATTATTATTCA
11075 ACCCATCTAA
Statistics
Matches: 150, Mismatches: 26, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
80 6 0.04
81 58 0.39
82 56 0.37
83 26 0.17
84 2 0.01
85 2 0.01
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (81 bp):
GTTTTCCATTATTATTCAGAGAATCTCTGACATGTCATAGTGTTTCATCCCATCCGAAATGAAAG
ACGCATTAAGGGAAAC
Found at i:11232 original size:82 final size:82
Alignment explanation
Indices: 11085--11341 Score: 318
Period size: 82 Copynumber: 3.1 Consensus size: 82
11075 ACCCATCTAA
* * **
11085 AAATGAAAGGAGCGTTCCAGGAGAAGTGTTTTCCATTATTATTCAGAGAATCTCTACCATGTCAT
1 AAATGAAAGGAGCATTCCAGG-GAAGCGTTTTCCATTATTATTCAGAGAATCTCTGTCATGTCAT
* *
11150 AGTGTTCCACCCCATCCG
65 AGTGTTTCATCCCATCCG
* *
11168 AAATGAAAGGTGCATTCCAGGGAAGCGTTTTCCATTATTATTCAGAGAATCTCTGTCATTTCATA
1 AAATGAAAGGAGCATTCCAGGGAAGCGTTTTCCATTATTATTCAGAGAATCTCTGTCATGTCATA
* *
11233 ATGTTTCATCCCATCCA
66 GTGTTTCATCCCATCCG
* * * * *
11250 AAATGAAAAGAGCTTTCCAAGGGAAGCATTTTCCATTATTATT-AAAGAATCTTTGTCATGTCAT
1 AAATGAAAGGAGCATTCC-AGGGAAGCGTTTTCCATTATTATTCAGAGAATCTCTGTCATGTCAT
* ** *
11314 AGTATTTCATCATATCTG
65 AGTGTTTCATCCCATCCG
11332 AAATGAAAGG
1 AAATGAAAGG
11342 TGCTTGTTCC
Statistics
Matches: 149, Mismatches: 24, Indels: 3
0.85 0.14 0.02
Matches are distributed among these distances:
82 107 0.72
83 42 0.28
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (82 bp):
AAATGAAAGGAGCATTCCAGGGAAGCGTTTTCCATTATTATTCAGAGAATCTCTGTCATGTCATA
GTGTTTCATCCCATCCG
Found at i:11284 original size:220 final size:219
Alignment explanation
Indices: 10894--11292 Score: 581
Period size: 220 Copynumber: 1.8 Consensus size: 219
10884 TAGGGAAACA
* * *
10894 TTTTCCTTTATTATTCAGATAATCTCTTACATGTCATAGTGTTCCATCCCATCCGAAATGAAATG
1 TTTTCCATTATTATTCAGAGAATCTCTTACATGTCATAGTGTTCCACCCCATCCGAAATGAAATG
* * *
10959 CATTCCAGGGGAAACGTTTTCCATTATTATTGAAAGGATATATGTCATATCATAGTGTTTCATCC
66 CATTCCAGGGGAAACGTTTTCCATTATTATTCAAAGAATATATGTCATATCATAATGTTTCATCC
* * *
11024 CATCCGAAATGAAAGGTACGGTTCAAGGGAAACGTTTTCCATTATTATTCAACCCATCTAAAAAT
131 CATCCAAAATGAAAAGTACGGTTCAAGGGAAACATTTTCCATTATTATTCAACCCATCTAAAAAT
11089 GAAAGGAGCGTTCCAGGAGAAGTG
196 GAAAGGAGCGTTCCAGGAGAAGTG
11113 TTTTCCATTATTATTCAGAGAATCTC-TACCATGTCATAGTGTTCCACCCCATCCGAAATGAAAG
1 TTTTCCATTATTATTCAGAGAATCTCTTA-CATGTCATAGTGTTCCACCCCATCCGAAATGAAA-
* * * * *
11177 GTGCATTCCA-GGGAAGCGTTTTCCATTATTATTCAGAGAATCTCTGTCATTTCATAATGTTTCA
64 -TGCATTCCAGGGGAAACGTTTTCCATTATTATTCAAAGAATATATGTCATATCATAATGTTTCA
* *
11241 TCCCATCCAAAATGAAAAG-A-GCTTTCCAAGGGAAGCATTTTCCATTATTATT
128 TCCCATCCAAAATGAAAAGTACG-GTT-CAAGGGAAACATTTTCCATTATTATT
11293 AAAGAATCTT
Statistics
Matches: 159, Mismatches: 16, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
218 3 0.02
219 60 0.38
220 87 0.55
221 9 0.06
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (219 bp):
TTTTCCATTATTATTCAGAGAATCTCTTACATGTCATAGTGTTCCACCCCATCCGAAATGAAATG
CATTCCAGGGGAAACGTTTTCCATTATTATTCAAAGAATATATGTCATATCATAATGTTTCATCC
CATCCAAAATGAAAAGTACGGTTCAAGGGAAACATTTTCCATTATTATTCAACCCATCTAAAAAT
GAAAGGAGCGTTCCAGGAGAAGTG
Found at i:11489 original size:30 final size:29
Alignment explanation
Indices: 11454--11512 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 29
11444 CAATTTAAGG
11454 CAAAATGGT-TTTGGACTTGAATTGAATTTA
1 CAAAAT-GTATTTGGACTT-AATTGAATTTA
11484 CAAAATGTATTTGGACTTAATTGAATTTA
1 CAAAATGTATTTGGACTTAATTGAATTTA
11513 TTCAAAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 13 0.46
30 15 0.54
ACGTcount: A:0.36, C:0.07, G:0.17, T:0.41
Consensus pattern (29 bp):
CAAAATGTATTTGGACTTAATTGAATTTA
Found at i:11735 original size:21 final size:21
Alignment explanation
Indices: 11709--11750 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
11699 ATTTGAATAT
*
11709 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
11730 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
11751 CCCATTCTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:12041 original size:34 final size:32
Alignment explanation
Indices: 12002--12071 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
11992 TTTTGTAAAG
* *
12002 GGGAAATGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
12036 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
12068 GGGA
1 GGGA
12072 GTTTGTAAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.23
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:13325 original size:65 final size:63
Alignment explanation
Indices: 13209--13416 Score: 199
Period size: 65 Copynumber: 3.2 Consensus size: 63
13199 TTTCAAAGTG
* * **
13209 ATGCACCGATGCACCAATCCATGCATCGATGCAC-CATGGAATAAATT-AAACATCAAATGCATT
1 ATGCATCGATGCA-CAA-CCATGCATCGATGCACTCA-GG-CTATTTTGAAACATCAAATGCATT
13272 TC
62 TC
* * *
13274 ATGCATCAATGCACATACTATGCATCGATGCACTCAGAG-T-TTTATGAAAACATCACATGCATT
1 ATGCATCGATGCACA-ACCATGCATCGATGCACTCAG-GCTATTT-TG-AAACATCAAATGCATT
*
13337 TG
62 TC
* * * *
13339 ATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATTCATTTC
1 ATGCATCGATGCA-CAACCATGCATCGATGCACTCAGGCTATTTTGAAACATCAAATGCATTTC
13403 ATGCATCGATGCAC
1 ATGCATCGATGCAC
13417 TCTTAGTGAA
Statistics
Matches: 119, Mismatches: 15, Indels: 20
0.77 0.10 0.13
Matches are distributed among these distances:
62 1 0.01
63 3 0.03
64 46 0.39
65 64 0.54
66 5 0.04
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.27
Consensus pattern (63 bp):
ATGCATCGATGCACAACCATGCATCGATGCACTCAGGCTATTTTGAAACATCAAATGCATTTC
Found at i:13668 original size:7 final size:7
Alignment explanation
Indices: 13656--13681 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
13646 CAAGAAAACA
13656 CAAGAAT
1 CAAGAAT
13663 CAAGAAT
1 CAAGAAT
13670 CAAGAAT
1 CAAGAAT
13677 CAAGA
1 CAAGA
13682 GAGAATCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.15, G:0.15, T:0.12
Consensus pattern (7 bp):
CAAGAAT
Found at i:19229 original size:21 final size:22
Alignment explanation
Indices: 19182--19258 Score: 68
Period size: 21 Copynumber: 3.4 Consensus size: 22
19172 CACTTAACAT
* *
19182 TGCATCGATACATCCCTTTGAATG
1 TGCATCGATACA--CCTATGAAGG
19206 TGCATCGATACA-CTATGAAGG
1 TGCATCGATACACCTATGAAGG
* *
19227 TGCATCGATGAACGCCT-TGAATG
1 TGCATCGAT--ACACCTATGAAGG
19250 TGCATCGAT
1 TGCATCGAT
19259 GCACAAGGCC
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
21 16 0.35
23 16 0.35
24 14 0.30
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (22 bp):
TGCATCGATACACCTATGAAGG
Found at i:19252 original size:23 final size:21
Alignment explanation
Indices: 19199--19259 Score: 70
Period size: 23 Copynumber: 2.8 Consensus size: 21
19189 ATACATCCCT
19199 TTGAATGTGCATCGAT-ACAC
1 TTGAATGTGCATCGATGACAC
* *
19219 TATGAAGGTGCATCGATGAACGCC
1 T-TGAATGTGCATCGATG-AC-AC
19243 TTGAATGTGCATCGATG
1 TTGAATGTGCATCGATG
19260 CACAAGGCCA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
20 1 0.03
21 14 0.41
23 17 0.50
24 2 0.06
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Consensus pattern (21 bp):
TTGAATGTGCATCGATGACAC
Found at i:22112 original size:57 final size:56
Alignment explanation
Indices: 22043--22149 Score: 137
Period size: 56 Copynumber: 1.9 Consensus size: 56
22033 TGCACATACT
* * *
22043 ATGCATCAATGCACT-TAGAGT-TTTATGAAAACATCGAATGCATTTGATGCACCAGCC
1 ATGCATCAATGCACTAT-GACTATTT-TG-AAACATCGAATACATTTCATGCACCAGCC
*
22100 ATGCATCGATGCACTATGACTATTTTGAAACATCGAATACATTTCATGCA
1 ATGCATCAATGCACTATGACTATTTTGAAACATCGAATACATTTCATGCA
22150 TCGATGCACT
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
56 21 0.48
57 19 0.43
58 4 0.09
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.30
Consensus pattern (56 bp):
ATGCATCAATGCACTATGACTATTTTGAAACATCGAATACATTTCATGCACCAGCC
Found at i:24331 original size:330 final size:330
Alignment explanation
Indices: 23283--24930 Score: 3038
Period size: 330 Copynumber: 5.0 Consensus size: 330
23273 TATATCGTGG
23283 AATAGAGTTCACATCTAAAGAAGAAACAATTATGTCAATTAAGAATTACAATATTCGTAATTCAG
1 AATAGAGTTCACATCTAAAGAAGAAACAATTATGTCAATTAAGAATTACAATATTCGTAATTCAG
23348 TT-AGTCCAGAGTCGATCGATCTACCACCAAAAAGTATGTTTGTTATTGTGTCCAACGTGATAAC
66 TTCAGTCCAGAGTCGATCGATCTACCACCAAAAAGTATGTTTGTTATTGTGTCCAACGTGATAAC
*
23412 GGATGCAATT-GATAGTTTGTATTTCAAAGAAGAAGAATACTGATATA-AGGAACTAACAAAATA
131 GGATGCAATTGGATAGTTTGTGTTTCAAAGAAGAAGAATACTGATATATAGGAACTAACAAAATA
*
23475 CAACAGTCCCCATACATGTTATGCACAGGATATCAACTAGAACCATCTAAACTTGGACTCCAACG
196 CAACAGTCCCCATACATGTTGTGCACAGGATATCAACTAGAACCATCTAAACTTGGACTCCAACG
*
23540 TGATTTGCCAAACTATCATGCCCTTGGTCAGAGCAAGCTCTCATATACCTATTGCAATGTTGATT
261 TGATTTGCCAAACTATCATGCCCTTGGTCAGAGCAAGCTCCCATATACCTATTGCAATGTTGATT
23605 TCTGC
326 TCTGC
*
23610 AATAGAGTTCACATCTAAAGAAGAAACAATTATGTCAATTAAGAATTATAATATTCGTAATTCAG
1 AATAGAGTTCACATCTAAAGAAGAAACAATTATGTCAATTAAGAATTACAATATTCGTAATTCAG
* *
23675 TTCAGTCCAGAGTCGATCGATCTGCCACCAAAAAGTATGTTTGTTACTGTGTCCAACGTGATAAC
66 TTCAGTCCAGAGTCGATCGATCTACCACCAAAAAGTATGTTTGTTATTGTGTCCAACGTGATAAC
23740 GGATGCAATTGGATAGTTTGTGTTTCAAAGAAGAAGAATACTGATATATAGGAACTAACAAAATA
131 GGATGCAATTGGATAGTTTGTGTTTCAAAGAAGAAGAATACTGATATATAGGAACTAACAAAATA
*
23805 CAACAGTCCCCATACATATTGTGCACA-GATAT-AACTAGAACCATCTAAACTTGGACTCCAACG
196 CAACAGTCCCCATACATGTTGTGCACAGGATATCAACTAGAACCATCTAAACTTGGACTCCAACG
23868 TGATTTGCCAAACTATCATGCCCTTGGTCAGAGCAAGCTCCCATATACCTATTGCAATGTTGATT
261 TGATTTGCCAAACTATCATGCCCTTGGTCAGAGCAAGCTCCCATATACCTATTGCAATGTTGATT
23933 TCTGC
326 TCTGC
*
23938 AATAGAGTTCACATCTAAAGAAGAAACAATTATGTCAATTAAGAATTACAATATTCATAATTCAG
1 AATAGAGTTCACATCTAAAGAAGAAACAATTATGTCAATTAAGAATTACAATATTCGTAATTCAG
*
24003 TTCAGTCCAGAGTCGATCGATCTACCACCAAAAATTATGTTTGTTATTGTGTCCAACGTGATAAC
66 TTCAGTCCAGAGTCGATCGATCTACCACCAAAAAGTATGTTTGTTATTGTGTCCAACGTGATAAC
* *
24068 GGATGCAATTGGATAGTTTGTGTTTCAAAGAAGAAGAATATTGATATATAGGAACTAATAAAATA
131 GGATGCAATTGGATAGTTTGTGTTTCAAAGAAGAAGAATACTGATATATAGGAACTAACAAAATA
24133 CAACAGTCCCCATACATGTTGTGCACAGGATATCAACTAGAACCATCTAAACTTGGACTCCAACG
196 CAACAGTCCCCATACATGTTGTGCACAGGATATCAACTAGAACCATCTAAACTTGGACTCCAACG
*
24198 TGATTTGCCAAACTATCATGCCCTTGGTCAGAGTAAGCTCCCATATACCTATTGCAATGTTGATT
261 TGATTTGCCAAACTATCATGCCCTTGGTCAGAGCAAGCTCCCATATACCTATTGCAATGTTGATT
**
24263 TCTAT
326 TCTGC
24268 AATAGAGTTCACATCTAAAGAAGAAACAATTATGTCAATTAAGAATTACAATATTCGTAATTCAG
1 AATAGAGTTCACATCTAAAGAAGAAACAATTATGTCAATTAAGAATTACAATATTCGTAATTCAG
*
24333 TTCAGTCCAGAGTCGATCGATCTACCACCAAAAAGTATGTTTGTTATTGTGTCCAACGTGATAAA
66 TTCAGTCCAGAGTCGATCGATCTACCACCAAAAAGTATGTTTGTTATTGTGTCCAACGTGATAAC
*
24398 GGATGCAATTGGATAGTTTGTGTTTCAAAGAAGAAGAATATTGATATATAGGAACTAACAAAATA
131 GGATGCAATTGGATAGTTTGTGTTTCAAAGAAGAAGAATACTGATATATAGGAACTAACAAAATA
24463 CAACAGTCCCCATACATGTTGTGCACAGGATATCAACTAGAACCATCTAAACTTGGACTCCAACG
196 CAACAGTCCCCATACATGTTGTGCACAGGATATCAACTAGAACCATCTAAACTTGGACTCCAACG
* *
24528 TGATTTGCCAAACTATCATGCCCTTGGTCAGAGCAAGTTCCCATATACCTATTGCAATGTTAATT
261 TGATTTGCCAAACTATCATGCCCTTGGTCAGAGCAAGCTCCCATATACCTATTGCAATGTTGATT
* *
24593 TATGT
326 TCTGC
24598 AATAGAGTTCACATCTAAAGAAGAAACAATTATGTCAATTAAGAATTACAATATTCGTAATTCAG
1 AATAGAGTTCACATCTAAAGAAGAAACAATTATGTCAATTAAGAATTACAATATTCGTAATTCAG
24663 TTCAGTCCAGAGTCGATCGATCTACCACCAAAAAGTATGTTTGTTATTGTGTCCAACGTGATAAC
66 TTCAGTCCAGAGTCGATCGATCTACCACCAAAAAGTATGTTTGTTATTGTGTCCAACGTGATAAC
* *
24728 GAATGCAATTGGATAGTTTATGTTTCAAAGAAGAAGAATACTGATATATAGGAACTAACAAAATA
131 GGATGCAATTGGATAGTTTGTGTTTCAAAGAAGAAGAATACTGATATATAGGAACTAACAAAATA
* *
24793 CAACAGT-CCCATACATGTTGTGCACAGGATATTAACTAGAATCATCTAAACTTGGACTCCAACG
196 CAACAGTCCCCATACATGTTGTGCACAGGATATCAACTAGAACCATCTAAACTTGGACTCCAACG
24857 TGATTTGCCAAACTATCATGCCCTTGGTCAGAGCAAGCTCCCATATACCTATTGCAATGTTGATT
261 TGATTTGCCAAACTATCATGCCCTTGGTCAGAGCAAGCTCCCATATACCTATTGCAATGTTGATT
24922 TCTGC
326 TCTGC
24927 AATA
1 AATA
24931 CAATCTCAAT
Statistics
Matches: 1279, Mismatches: 37, Indels: 8
0.97 0.03 0.01
Matches are distributed among these distances:
327 66 0.05
328 384 0.30
329 171 0.13
330 658 0.51
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.29
Consensus pattern (330 bp):
AATAGAGTTCACATCTAAAGAAGAAACAATTATGTCAATTAAGAATTACAATATTCGTAATTCAG
TTCAGTCCAGAGTCGATCGATCTACCACCAAAAAGTATGTTTGTTATTGTGTCCAACGTGATAAC
GGATGCAATTGGATAGTTTGTGTTTCAAAGAAGAAGAATACTGATATATAGGAACTAACAAAATA
CAACAGTCCCCATACATGTTGTGCACAGGATATCAACTAGAACCATCTAAACTTGGACTCCAACG
TGATTTGCCAAACTATCATGCCCTTGGTCAGAGCAAGCTCCCATATACCTATTGCAATGTTGATT
TCTGC
Found at i:30340 original size:20 final size:21
Alignment explanation
Indices: 30315--30366 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
30305 TTTTCCCAAT
*
30315 TCGCAATGCGAATAAG-TAAA
1 TCGCAATGCGAATAAGAAAAA
* **
30335 TCGCAACGCGAATTGGAAAAA
1 TCGCAATGCGAATAAGAAAAA
30356 TCGCAATGCGA
1 TCGCAATGCGA
30367 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 13 0.50
21 13 0.50
ACGTcount: A:0.40, C:0.19, G:0.23, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATAAGAAAAA
Found at i:30380 original size:20 final size:20
Alignment explanation
Indices: 30355--30468 Score: 113
Period size: 20 Copynumber: 5.7 Consensus size: 20
30345 AATTGGAAAA
*
30355 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
30375 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTGACT
* * *
30395 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
30416 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
30436 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
30456 TTCGCAACGCGAT
1 ATCGCAACGCGAT
30469 TTACATAGCG
Statistics
Matches: 81, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
19 2 0.02
20 64 0.79
21 13 0.16
22 2 0.02
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:30399 original size:61 final size:61
Alignment explanation
Indices: 30352--30468 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
30342 GCGAATTGGA
* * * * *
30352 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * *
30413 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGAT
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGAT
30469 TTACATAGCG
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:31071 original size:19 final size:19
Alignment explanation
Indices: 31024--31065 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
31014 ACGAGAGAAT
*
31024 CGCAACGCGAAATAAAAAA
1 CGCAACGCGAAACAAAAAA
*
31043 CGCAACGCGAAACAAAAAT
1 CGCAACGCGAAACAAAAAA
31062 CGCA
1 CGCA
31066 TTGCGATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.52, C:0.26, G:0.17, T:0.05
Consensus pattern (19 bp):
CGCAACGCGAAACAAAAAA
Found at i:31083 original size:19 final size:19
Alignment explanation
Indices: 31061--31243 Score: 170
Period size: 19 Copynumber: 10.1 Consensus size: 19
31051 GAAACAAAAA
*
31061 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
31080 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
31099 TCGTGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
31118 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
31137 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * **
31151 TCTCGTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
31170 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
31184 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
31203 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
31223 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
31243 T
1 T
31244 TAACCAAAAG
Statistics
Matches: 134, Mismatches: 18, Indels: 24
0.76 0.10 0.14
Matches are distributed among these distances:
14 19 0.14
16 4 0.03
17 5 0.04
19 74 0.55
20 31 0.23
21 1 0.01
ACGTcount: A:0.12, C:0.22, G:0.21, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:31119 original size:38 final size:38
Alignment explanation
Indices: 31061--31243 Score: 170
Period size: 33 Copynumber: 5.0 Consensus size: 38
31051 GAAACAAAAA
*
31061 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* *
31099 TCGTGTTGCGATTTTTATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* * **
31137 TCGCGTTGCGA--TTC---TCTCGTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* **
31170 TCGCGTTGCGA--TTC---TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* *
31203 TCCGCGTTGCGATTCTCATTATCTCGTTGCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT-TCGCGTTGCGATTTTCATT
31243 T
1 T
31244 TAACCAAAAG
Statistics
Matches: 125, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
33 48 0.38
34 10 0.08
36 4 0.03
38 45 0.36
40 18 0.14
ACGTcount: A:0.12, C:0.22, G:0.21, T:0.45
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
Found at i:33321 original size:42 final size:42
Alignment explanation
Indices: 33245--33333 Score: 106
Period size: 42 Copynumber: 2.1 Consensus size: 42
33235 GACTCGCCTG
* *
33245 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCACTCCCACCGTTGAAGAGGCCCCTA
* * * * * *
33287 TCATTCCTCGAGAGTCCCCTCCCACCGTTTAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCACTCCCACCGTTGAAGAGGCCCCTA
33329 TCATC
1 TCATC
33334 GTTGAAGAGG
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.21, C:0.37, G:0.17, T:0.25
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCACTCCCACCGTTGAAGAGGCCCCTA
Found at i:34732 original size:14 final size:14
Alignment explanation
Indices: 34713--34748 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
34703 ATTGTTTAAT
34713 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
34727 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
34741 TGATTTGT
1 TGATTTGT
34749 TTAATTGATG
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:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:34938 original size:38 final size:33
Alignment explanation
Indices: 34863--34949 Score: 102
Period size: 38 Copynumber: 2.5 Consensus size: 33
34853 CTATCGTAAT
*
34863 GCGAAATGAAAATCGCAACGAGAGAATCGCAAC
1 GCGAAATGAAAATCGCAACGAGAAAATCGCAAC
34896 GCGAAATGAAAATCGCAACGCGAAATGAAAATCGCAAC
1 GCGAAATGAAAATCGCAA--CG--A-GAAAATCGCAAC
* *
34934 GCGAAATTAAATTCGC
1 GCGAAATGAAAATCGC
34950 GTTGCGATTT
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
33 18 0.39
35 2 0.04
37 1 0.02
38 25 0.54
ACGTcount: A:0.45, C:0.21, G:0.22, T:0.13
Consensus pattern (33 bp):
GCGAAATGAAAATCGCAACGAGAAAATCGCAAC
Found at i:34949 original size:19 final size:19
Alignment explanation
Indices: 34863--34940 Score: 112
Period size: 19 Copynumber: 4.4 Consensus size: 19
34853 CTATCGTAAT
34863 GCGAAATGAAAATCGCAA-
1 GCGAAATGAAAATCGCAAC
*
34881 -CG--A-GAGAATCGCAAC
1 GCGAAATGAAAATCGCAAC
34896 GCGAAATGAAAATCGCAAC
1 GCGAAATGAAAATCGCAAC
34915 GCGAAATGAAAATCGCAAC
1 GCGAAATGAAAATCGCAAC
34934 GCGAAAT
1 GCGAAAT
34941 TAAATTCGCG
Statistics
Matches: 53, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
14 10 0.19
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 37 0.70
ACGTcount: A:0.46, C:0.21, G:0.23, T:0.10
Consensus pattern (19 bp):
GCGAAATGAAAATCGCAAC
Found at i:34967 original size:19 final size:19
Alignment explanation
Indices: 34945--35095 Score: 80
Period size: 19 Copynumber: 8.7 Consensus size: 19
34935 CGAAATTAAA
34945 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
34964 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
34979 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
34997 TTCGCATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
*
35011 TTAGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
35030 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
35045 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
35063 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
35082 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
35096 AGACATTAAG
Statistics
Matches: 95, Mismatches: 21, Indels: 31
0.65 0.14 0.21
Matches are distributed among these distances:
14 28 0.29
16 6 0.06
17 6 0.06
19 45 0.47
20 10 0.11
ACGTcount: A:0.15, C:0.23, G:0.21, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:34991 original size:33 final size:32
Alignment explanation
Indices: 34949--35075 Score: 193
Period size: 33 Copynumber: 3.9 Consensus size: 32
34939 ATTAAATTCG
34949 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
34982 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
35015 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
35048 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
35076 AGTAATTTCC
Statistics
Matches: 86, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
31 3 0.03
33 80 0.93
35 3 0.03
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:35038 original size:66 final size:66
Alignment explanation
Indices: 34942--35074 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
34932 ACGCGAAATT
*
34942 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
35007 G
66 G
*
35008 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
35073 G
66 G
35074 A
1 A
35075 TAGTAATTTC
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.17, C:0.23, G:0.20, T:0.41
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:37384 original size:12 final size:12
Alignment explanation
Indices: 37367--37391 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
37357 TCTTCGGGGA
37367 CTTTTTCTTCTT
1 CTTTTTCTTCTT
37379 CTTTTTCTTCTT
1 CTTTTTCTTCTT
37391 C
1 C
37392 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:38701 original size:20 final size:20
Alignment explanation
Indices: 38676--38713 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
38666 ATTCATTTGA
*
38676 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGAGAAAATGG
38696 CTATCGCAACGAGAAAAT
1 CTATCGCAACGAGAAAAT
38714 CGCAATGCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.24, G:0.21, T:0.16
Consensus pattern (20 bp):
CTATCGCAACGAGAAAATGG
Found at i:38773 original size:19 final size:19
Alignment explanation
Indices: 38732--38799 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
38722 GAAATGAAAA
38732 TCGCATTGCGATTTTC--T
1 TCGCATTGCGATTTTCATT
38749 T-G--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
38765 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
38784 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
38800 TCGTTGCGAT
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
14 11 0.24
16 3 0.07
17 2 0.04
19 30 0.65
ACGTcount: A:0.13, C:0.21, G:0.18, T:0.49
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:38775 original size:52 final size:52
Alignment explanation
Indices: 38713--38827 Score: 122
Period size: 52 Copynumber: 2.2 Consensus size: 52
38703 AACGAGAAAA
* * ***
38713 TCGCAATGCGAAATGAAAATCGCATTGCGATTTTCTTGTTGCGATTTTCATT
1 TCGCATTGCGAAATGAAAATCGCATTGCGATTTTCTCGTTGCGATAGCCATT
** ** **
38765 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCTCGTTGCGATAGCCATT
1 TCGCATTGCGAAATGAAAATCGCATTGCGATTTTCTCGTTGCGATAGCCATT
*
38817 TCGCGTTGCGA
1 TCGCATTGCGA
38828 TAGTCTGTTT
Statistics
Matches: 51, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.39
Consensus pattern (52 bp):
TCGCATTGCGAAATGAAAATCGCATTGCGATTTTCTCGTTGCGATAGCCATT
Found at i:38935 original size:14 final size:14
Alignment explanation
Indices: 38916--38952 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
38906 CATCAATTAA
38916 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
38930 ACAAATCATCTTTT
1 ACAAATCAACATTT
38944 ACAAATCAA
1 ACAAATCAA
38953 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:40842 original size:20 final size:19
Alignment explanation
Indices: 40819--40886 Score: 82
Period size: 20 Copynumber: 3.5 Consensus size: 19
40809 GAAACTTAAA
40819 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCG-AAATGACT
*
40839 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
40859 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
40878 ATCGCAACG
1 ATCGCAACG
40887 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
19 14 0.34
20 26 0.63
21 1 0.02
ACGTcount: A:0.38, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:40894 original size:14 final size:14
Alignment explanation
Indices: 40875--40932 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
40865 ATGCGAAATG
40875 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
40889 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
40905 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
40921 AAAATCGCAACG
1 AAAATCGCAACG
40933 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:40917 original size:32 final size:33
Alignment explanation
Indices: 40859--40947 Score: 162
Period size: 32 Copynumber: 2.7 Consensus size: 33
40849 GGAAATGGCT
*
40859 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
40892 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
40924 ATCGCAACGCGAAATGAAAATCGC
1 ATCGCAACGCGAAATGAAAATCGC
40948 CGCGTTGCGA
Statistics
Matches: 54, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
32 32 0.59
33 22 0.41
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:40969 original size:14 final size:14
Alignment explanation
Indices: 40950--41007 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
40940 AAAATCGCCG
40950 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
40964 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
40980 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
40996 CGTTGCGATTTT
1 CGTTGCGATTTT
41008 CATTTCGTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:40993 original size:32 final size:33
Alignment explanation
Indices: 40952--41023 Score: 128
Period size: 32 Copynumber: 2.2 Consensus size: 33
40942 AATCGCCGCG
40952 TTGCGATTTTGTCGTTGCGA-TTTCATTTCGCA
1 TTGCGATTTTGTCGTTGCGATTTTCATTTCGCA
*
40984 TTGCGATTTTGTCGTTGCGATTTTCATTTCGTA
1 TTGCGATTTTGTCGTTGCGATTTTCATTTCGCA
41017 TTGCGAT
1 TTGCGAT
41024 AGCCATTTCC
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 20 0.53
33 18 0.47
ACGTcount: A:0.12, C:0.17, G:0.22, T:0.49
Consensus pattern (33 bp):
TTGCGATTTTGTCGTTGCGATTTTCATTTCGCA
Found at i:41022 original size:19 final size:17
Alignment explanation
Indices: 40966--41023 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 17
40956 GATTTTGTCG
40966 TTGCGATTTCATTTCGCA
1 TTGCGATTTCATTTCG-A
*
40984 TTGCGATTT--TGTCG-
1 TTGCGATTTCATTTCGA
40998 TTGCGATTTTCATTTCGTA
1 TTGCGA-TTTCATTTCG-A
41017 TTGCGAT
1 TTGCGAT
41024 AGCCATTTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 6 0.18
15 3 0.09
16 4 0.12
17 4 0.12
18 10 0.30
19 6 0.18
ACGTcount: A:0.14, C:0.17, G:0.21, T:0.48
Consensus pattern (17 bp):
TTGCGATTTCATTTCGA
Found at i:41042 original size:20 final size:20
Alignment explanation
Indices: 41017--41062 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
41007 TCATTTCGTA
41017 TTGCGATAGCCATTTCCGCG
1 TTGCGATAGCCATTTCCGCG
* * *
41037 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGCCATTTCCGCG
41057 TTGCGA
1 TTGCGA
41063 AAGTAAACTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.15, C:0.22, G:0.26, T:0.37
Consensus pattern (20 bp):
TTGCGATAGCCATTTCCGCG
Found at i:41570 original size:18 final size:18
Alignment explanation
Indices: 41544--41588 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
41534 GTCGATCAGA
*
41544 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
41562 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
41580 TGATGGCTC
1 TGATGGCTC
41589 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:42941 original size:20 final size:20
Alignment explanation
Indices: 42908--42965 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
42898 AATAGTTTCT
**
42908 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACAC
**
42928 GAAAATGACTATCGCAATGC
1 GAAAATGACTATCGCAACAC
**
42948 GAATTTGACTATCGCAAC
1 GAAAATGACTATCGCAAC
42966 GAGACAATCG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.43, C:0.21, G:0.17, T:0.19
Consensus pattern (20 bp):
GAAAATGACTATCGCAACAC
Found at i:43485 original size:20 final size:20
Alignment explanation
Indices: 43460--43512 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
43450 GATTATGTAT
*
43460 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTAAG
43480 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTAAG
*
43500 TATCTCGTTGCGA
1 TATCGCGTTGCGA
43513 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTAAG
Found at i:44359 original size:21 final size:20
Alignment explanation
Indices: 44315--44359 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
44305 TTTATGGATT
* *
44315 GAATATCGATATTCAAGTGA
1 GAATATCGATACTCAAGGGA
*
44335 GAATATCGATAGCTCACGGGA
1 GAATATCGATA-CTCAAGGGA
44356 GAAT
1 GAAT
44360 TGATATAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.38, C:0.13, G:0.24, T:0.24
Consensus pattern (20 bp):
GAATATCGATACTCAAGGGA
Found at i:45035 original size:31 final size:30
Alignment explanation
Indices: 44992--45053 Score: 72
Period size: 31 Copynumber: 2.0 Consensus size: 30
44982 AAAATTAACT
*
44992 ATTAATTAAAATT-TATTTTCTTTTAATAAA
1 ATTAATTAAAATTATAATTT-TTTTAATAAA
* *
45022 ATTATATTTAAATTATAATTTTTTTATTAAA
1 ATTA-ATTAAAATTATAATTTTTTTAATAAA
45053 A
1 A
45054 ACAATAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
30 4 0.15
31 18 0.67
32 5 0.19
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (30 bp):
ATTAATTAAAATTATAATTTTTTTAATAAA
Found at i:49364 original size:17 final size:17
Alignment explanation
Indices: 49344--49376 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
49334 TTTATACTAT
49344 TTATGTGTTG-TTTTATC
1 TTAT-TGTTGATTTTATC
49361 TTATTGTTGATTTTAT
1 TTATTGTTGATTTTAT
49377 GGATTTGGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.15, C:0.03, G:0.15, T:0.67
Consensus pattern (17 bp):
TTATTGTTGATTTTATC
Done.