Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003647.1 Hibiscus syriacus cultivar Beakdansim tig00007753_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: 66821
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:1427 original size:64 final size:63
Alignment explanation
Indices: 1359--1502 Score: 157
Period size: 64 Copynumber: 2.3 Consensus size: 63
1349 TGCATTTGTG
* * ** *
1359 CACAAATTACATTTGATGTTTC-AATGAGCCTGGAGTGCATCGATGCA-TGGTATGTGCATCGGT
1 CACAAAATACATTCGATG-TTCAAAT-AGCCAAGAGTGCATCGATGCATTGCT-TGTGCATCGGT
1422 A
63 A
* **
1423 CACAAAATGCATTCGATGTTCAAAATATTCAAGAGTGCATCGATGCATTGCTTGTGCATCGGTA
1 CACAAAATACATTCGATGTTC-AAATAGCCAAGAGTGCATCGATGCATTGCTTGTGCATCGGTA
*
1487 CACAAAATGCATTCGA
1 CACAAAATACATTCGA
1503 AATGGGTGTG
Statistics
Matches: 69, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
63 3 0.04
64 60 0.87
65 6 0.09
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.29
Consensus pattern (63 bp):
CACAAAATACATTCGATGTTCAAATAGCCAAGAGTGCATCGATGCATTGCTTGTGCATCGGTA
Found at i:15982 original size:6 final size:6
Alignment explanation
Indices: 15941--15984 Score: 54
Period size: 6 Copynumber: 7.2 Consensus size: 6
15931 AAAAGCAACA
*
15941 AAAATAG AAAAAG AAAGAAG AAAAAC AAAAAG -AAAAG AAAAAG A
1 AAAA-AG AAAAAG AAA-AAG AAAAAG AAAAAG AAAAAG AAAAAG A
15985 CTCCTACATC
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
5 5 0.15
6 18 0.55
7 10 0.30
ACGTcount: A:0.80, C:0.02, G:0.16, T:0.02
Consensus pattern (6 bp):
AAAAAG
Found at i:22700 original size:24 final size:24
Alignment explanation
Indices: 22669--22761 Score: 95
Period size: 24 Copynumber: 4.0 Consensus size: 24
22659 ACAACTGAAG
22669 AGAAGAAAATGAAACGAAAAAAAA
1 AGAAGAAAATGAAACGAAAAAAAA
*
22693 AGAAGAAAATGAAACGAAAAAAGA
1 AGAAGAAAATGAAACGAAAAAAAA
* * *
22717 AGAA-AAACTAAAAAAGAAAAAAGAA
1 AGAAGAAAAT-GAAACGAAAAAA-AA
*
22742 A-AAGAAAA-GAAA-GACAAAAA
1 AGAAGAAAATGAAACGAAAAAAA
22762 CATAAAAGAA
Statistics
Matches: 58, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
21 1 0.02
22 6 0.10
23 7 0.12
24 39 0.67
25 5 0.09
ACGTcount: A:0.76, C:0.04, G:0.16, T:0.03
Consensus pattern (24 bp):
AGAAGAAAATGAAACGAAAAAAAA
Found at i:22729 original size:17 final size:16
Alignment explanation
Indices: 22690--22749 Score: 54
Period size: 17 Copynumber: 3.7 Consensus size: 16
22680 AAACGAAAAA
22690 AAAAGAAGAAAATGAAACG
1 AAAA-AAGAAAA--AAACG
*
22709 AAAAAAGAAGAAAAACT
1 AAAAAAGAA-AAAAACG
22726 AAAAAAG-AAAAAA-G
1 AAAAAAGAAAAAAACG
22740 -AAAAAGAAAA
1 AAAAAAGAAAA
22750 GAAAGACAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
13 6 0.16
14 3 0.08
15 5 0.14
16 1 0.03
17 11 0.30
18 5 0.14
19 6 0.16
ACGTcount: A:0.78, C:0.03, G:0.15, T:0.03
Consensus pattern (16 bp):
AAAAAAGAAAAAAACG
Found at i:22768 original size:24 final size:22
Alignment explanation
Indices: 22671--22773 Score: 75
Period size: 24 Copynumber: 4.3 Consensus size: 22
22661 AACTGAAGAG
22671 AAGAAAATGAAACGAAAAAA-AAA
1 AAGAAAA-GAAA-GAAAAAACAAA
*
22694 GAAGAAAATGAAACGAAAAAAGAAGA
1 -AAGAAAA-GAAA-GAAAAAACAA-A
* *
22720 AA-AACTAAAAAAGAAAAAAGAAA
1 AAGAA--AAGAAAGAAAAAACAAA
22743 AAGAAAAGAAAGACAAAAACATAA
1 AAGAAAAGAAAGA-AAAAACA-AA
22767 AAGAAAA
1 AAGAAAA
22774 AGGGGTTAAG
Statistics
Matches: 69, Mismatches: 3, Indels: 14
0.80 0.03 0.16
Matches are distributed among these distances:
22 7 0.10
23 9 0.13
24 43 0.62
25 7 0.10
26 3 0.04
ACGTcount: A:0.77, C:0.05, G:0.15, T:0.04
Consensus pattern (22 bp):
AAGAAAAGAAAGAAAAAACAAA
Found at i:24093 original size:139 final size:139
Alignment explanation
Indices: 23764--24097 Score: 445
Period size: 139 Copynumber: 2.4 Consensus size: 139
23754 AATCATTTGT
* * * *
23764 GACCAGATCTTCTCAATGCGAAGGAGAAGCATCATCCTTAGACAACTAGACTTCCACATCACGTA
1 GACCAGATCTCCTCAACGCGAAGGAGAAGCGTCATCCTTAGACAACTAGACTTCCTCATCACGTA
* * * *
23829 GGAACCGTGTTGTCTCCAAATTATCCCTAAAGACGGCTAGACATCCTCATCACGTATGAACAATG
66 GGAACCGTATTGTCTCCAAATTATCCCTAAAGACGACTAGACATCCTCATCACATAAGAACAATG
* *
23894 TCGTCCATC
131 TCATCCACC
* * * * *
23903 GACCAAATCTCCTCAACGTGAAGGAGCAGCGTCATCATTAGAAAACTAGACTTCCTCATCACGTA
1 GACCAGATCTCCTCAACGCGAAGGAGAAGCGTCATCCTTAGACAACTAGACTTCCTCATCACGTA
* * *
23968 GGAACCGTATTGTCTCCAAATTATCCCTAAAGACGACTATACGTCCTCATCACATAAGAATAATG
66 GGAACCGTATTGTCTCCAAATTATCCCTAAAGACGACTAGACATCCTCATCACATAAGAACAATG
*
24033 TCATTCACC
131 TCATCCACC
* * * *
24042 GACCAGATCTCCTCAACGCGAAGGAGTAGTGTCACCCTCAGACAA-TCAGACTTCCT
1 GACCAGATCTCCTCAACGCGAAGGAGAAGCGTCATCCTTAGACAACT-AGACTTCCT
24098 TAATGCGAAG
Statistics
Matches: 167, Mismatches: 27, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
138 1 0.01
139 166 0.99
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.23
Consensus pattern (139 bp):
GACCAGATCTCCTCAACGCGAAGGAGAAGCGTCATCCTTAGACAACTAGACTTCCTCATCACGTA
GGAACCGTATTGTCTCCAAATTATCCCTAAAGACGACTAGACATCCTCATCACATAAGAACAATG
TCATCCACC
Found at i:24403 original size:107 final size:107
Alignment explanation
Indices: 24202--24396 Score: 275
Period size: 107 Copynumber: 1.8 Consensus size: 107
24192 TCTGAAAGCA
* * ** *
24202 ACCAGAACTCTTCAACACGGATAAGCAGAGTTTTCTTCAACACCAAATTATCTCCAGATTGATCC
1 ACCAGAACTATTCAACACGGATAAGAAGAGTCATCTTCAACACCAAATTATCTCCAGATTGACCC
* *
24267 GATTTCCTCAACGAGAATGAACAAAGTCATTTTTTTAACGCG
66 GACTTCCTCAAAGAGAATGAACAAAGTCATTTTTTTAACGCG
* * * *
24309 ACCAGATCTATTCAACATGGATGAGAAGAGTCATCTTCAACACCAAATTATCTTCAGATTGACCC
1 ACCAGAACTATTCAACACGGATAAGAAGAGTCATCTTCAACACCAAATTATCTCCAGATTGACCC
24374 GACTTCCTCAAA-AGGAATGAACA
66 GACTTCCTCAAAGA-GAATGAACA
24397 TTGTCATCTT
Statistics
Matches: 76, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
106 1 0.01
107 75 0.99
ACGTcount: A:0.35, C:0.24, G:0.14, T:0.26
Consensus pattern (107 bp):
ACCAGAACTATTCAACACGGATAAGAAGAGTCATCTTCAACACCAAATTATCTCCAGATTGACCC
GACTTCCTCAAAGAGAATGAACAAAGTCATTTTTTTAACGCG
Found at i:26160 original size:9 final size:9
Alignment explanation
Indices: 26148--26173 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
26138 TTTAGGCACT
26148 TTATTTTCG
1 TTATTTTCG
26157 TTATTTTCG
1 TTATTTTCG
26166 TTATTTTC
1 TTATTTTC
26174 AATTTGGTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.12, C:0.12, G:0.08, T:0.69
Consensus pattern (9 bp):
TTATTTTCG
Found at i:26308 original size:32 final size:32
Alignment explanation
Indices: 26263--26399 Score: 125
Period size: 32 Copynumber: 4.2 Consensus size: 32
26253 TCACTGACTT
* *
26263 ACTAACATCCTAACATTTATTTTATTGTTCAA
1 ACTAACATACTAACTTTTATTTTATTGTTCAA
**
26295 ACTAACATACTAACTTTTA-TTTATTTGTTCTT
1 ACTAACATACTAACTTTTATTTTA-TTGTTCAA
* * *
26327 ATTATCATACTAACTTTTTATTTTTATTGTT-ATC
1 ACTAACATACTAAC-TTTTA-TTTTATTGTTCA-A
* * *
26361 ACTAACTTACTAATCCTTTATTTTATTGTACAA
1 ACTAACATACTAA-CTTTTATTTTATTGTTCAA
26394 ACTAAC
1 ACTAAC
26400 CCCTAACTTT
Statistics
Matches: 84, Mismatches: 14, Indels: 13
0.76 0.13 0.12
Matches are distributed among these distances:
31 4 0.05
32 35 0.42
33 20 0.24
34 20 0.24
35 5 0.06
ACGTcount: A:0.31, C:0.17, G:0.03, T:0.49
Consensus pattern (32 bp):
ACTAACATACTAACTTTTATTTTATTGTTCAA
Found at i:26871 original size:2 final size:2
Alignment explanation
Indices: 26822--26851 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
26812 CTTTTTTTGC
26822 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
26852 TGCATGTTGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27091 original size:5 final size:5
Alignment explanation
Indices: 27072--27105 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
27062 TTTCACCTCG
27072 TTTTA TTTT- TATTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA T-TTTA TTTTA TTTTA TTTTA TTTT
27106 TAACTTTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 1 0.04
5 25 0.93
6 1 0.04
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTA
Found at i:28098 original size:21 final size:21
Alignment explanation
Indices: 28072--28126 Score: 110
Period size: 21 Copynumber: 2.6 Consensus size: 21
28062 CTTTATATAG
28072 TAGTATCGATACCATGAAGGA
1 TAGTATCGATACCATGAAGGA
28093 TAGTATCGATACCATGAAGGA
1 TAGTATCGATACCATGAAGGA
28114 TAGTATCGATACC
1 TAGTATCGATACC
28127 GTCAAGCCCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.25
Consensus pattern (21 bp):
TAGTATCGATACCATGAAGGA
Found at i:29382 original size:19 final size:17
Alignment explanation
Indices: 29334--29392 Score: 66
Period size: 18 Copynumber: 3.4 Consensus size: 17
29324 TATTAAATTT
*
29334 TATTTTTAGTATTTT-AA
1 TATTTTTAAT-TTTTAAA
*
29351 TATATTTAATTTTTAAAA
1 TATTTTTAATTTTT-AAA
29369 TATTTTTAAATTTTTAAA
1 TATTTTT-AATTTTTAAA
29387 TATTTT
1 TATTTT
29393 ATTTAAAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
16 4 0.11
17 8 0.22
18 17 0.47
19 7 0.19
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.63
Consensus pattern (17 bp):
TATTTTTAATTTTTAAA
Found at i:30013 original size:2 final size:2
Alignment explanation
Indices: 30006--30035 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
29996 TTAGACACAA
30006 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
30036 GAAAATATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:32898 original size:13 final size:13
Alignment explanation
Indices: 32880--32950 Score: 60
Period size: 13 Copynumber: 5.5 Consensus size: 13
32870 GGACTAACAA
32880 TGTGGTAATAGAT
1 TGTGGTAATAGAT
*
32893 TGTGGTTGAACA-A-
1 TGTGG-T-AATAGAT
32906 TGTGGTAATAGAT
1 TGTGGTAATAGAT
*
32919 TGTGGTTGAACA-A-
1 TGTGG-T-AATAGAT
32932 TGTGGTAATAGAT
1 TGTGGTAATAGAT
32945 TGTGGT
1 TGTGGT
32951 TAAGGTTTAG
Statistics
Matches: 46, Mismatches: 4, Indels: 16
0.70 0.06 0.24
Matches are distributed among these distances:
11 6 0.13
12 4 0.09
13 26 0.57
14 4 0.09
15 6 0.13
ACGTcount: A:0.28, C:0.03, G:0.32, T:0.37
Consensus pattern (13 bp):
TGTGGTAATAGAT
Found at i:32904 original size:26 final size:26
Alignment explanation
Indices: 32875--32951 Score: 154
Period size: 26 Copynumber: 3.0 Consensus size: 26
32865 AGACTGGACT
32875 AACAATGTGGTAATAGATTGTGGTTG
1 AACAATGTGGTAATAGATTGTGGTTG
32901 AACAATGTGGTAATAGATTGTGGTTG
1 AACAATGTGGTAATAGATTGTGGTTG
32927 AACAATGTGGTAATAGATTGTGGTT
1 AACAATGTGGTAATAGATTGTGGTT
32952 AAGGTTTAGA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 51 1.00
ACGTcount: A:0.31, C:0.04, G:0.30, T:0.35
Consensus pattern (26 bp):
AACAATGTGGTAATAGATTGTGGTTG
Found at i:40781 original size:12 final size:12
Alignment explanation
Indices: 40766--40831 Score: 80
Period size: 12 Copynumber: 5.6 Consensus size: 12
40756 GTTATTTAAA
40766 CGGGTATTGGGC
1 CGGGTATTGGGC
*
40778 CGGGTATTGGGT
1 CGGGTATTGGGC
*
40790 CGGGTATTGGGT
1 CGGGTATTGGGC
40802 C-GGTATTGGGC
1 CGGGTATTGGGC
** *
40813 CGGAAATCGGGC
1 CGGGTATTGGGC
40825 CGGGTAT
1 CGGGTAT
40832 ATATATATAT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
11 10 0.22
12 36 0.78
ACGTcount: A:0.12, C:0.15, G:0.47, T:0.26
Consensus pattern (12 bp):
CGGGTATTGGGC
Found at i:40793 original size:24 final size:24
Alignment explanation
Indices: 40766--40831 Score: 80
Period size: 23 Copynumber: 2.8 Consensus size: 24
40756 GTTATTTAAA
*
40766 CGGGTATTGGGCCGGGTATTGGGT
1 CGGGTATTGGGCCGGGTATTGGGC
*
40790 CGGGTATTGGGTC-GGTATTGGGC
1 CGGGTATTGGGCCGGGTATTGGGC
** *
40813 CGGAAATCGGGCCGGGTAT
1 CGGGTATTGGGCCGGGTAT
40832 ATATATATAT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
23 18 0.51
24 17 0.49
ACGTcount: A:0.12, C:0.15, G:0.47, T:0.26
Consensus pattern (24 bp):
CGGGTATTGGGCCGGGTATTGGGC
Found at i:40891 original size:24 final size:25
Alignment explanation
Indices: 40829--40891 Score: 71
Period size: 24 Copynumber: 2.6 Consensus size: 25
40819 TCGGGCCGGG
40829 TATATA-TATATATATTTAAATTAAA
1 TATATATTATAT-TATTTAAATTAAA
*
40854 TATATATT-TTTTATTTAAATTAAA
1 TATATATTATATTATTTAAATTAAA
40878 T-T-TATTAATATTAT
1 TATATATT-ATATTAT
40892 ATATATATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
22 4 0.12
23 1 0.03
24 19 0.58
25 8 0.24
26 1 0.03
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
TATATATTATATTATTTAAATTAAA
Found at i:40946 original size:8 final size:8
Alignment explanation
Indices: 40927--40969 Score: 63
Period size: 8 Copynumber: 5.6 Consensus size: 8
40917 ATTTATCGGG
40927 TCGGGT-A
1 TCGGGTAA
40934 TCGGGTAA
1 TCGGGTAA
40942 TCGGGT-A
1 TCGGGTAA
*
40949 GCGGGTAA
1 TCGGGTAA
40957 TCGGGTAA
1 TCGGGTAA
40965 TCGGG
1 TCGGG
40970 GCGGGGATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
7 12 0.38
8 20 0.62
ACGTcount: A:0.19, C:0.14, G:0.44, T:0.23
Consensus pattern (8 bp):
TCGGGTAA
Found at i:40947 original size:15 final size:15
Alignment explanation
Indices: 40927--40969 Score: 68
Period size: 15 Copynumber: 2.8 Consensus size: 15
40917 ATTTATCGGG
40927 TCGGGTATCGGGTAA
1 TCGGGTATCGGGTAA
*
40942 TCGGGTAGCGGGTAA
1 TCGGGTATCGGGTAA
40957 TCGGGTAATCGGG
1 TCGGGT-ATCGGG
40970 GCGGGGATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 20 0.80
16 5 0.20
ACGTcount: A:0.19, C:0.14, G:0.44, T:0.23
Consensus pattern (15 bp):
TCGGGTATCGGGTAA
Found at i:45253 original size:23 final size:24
Alignment explanation
Indices: 45223--45269 Score: 87
Period size: 23 Copynumber: 2.0 Consensus size: 24
45213 TATCTAAATT
45223 TAGTTAATGACAACAAAC-AGTTG
1 TAGTTAATGACAACAAACAAGTTG
45246 TAGTTAATGACAACAAACAAGTTG
1 TAGTTAATGACAACAAACAAGTTG
45270 ATTCAAGTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.45, C:0.13, G:0.17, T:0.26
Consensus pattern (24 bp):
TAGTTAATGACAACAAACAAGTTG
Found at i:46383 original size:29 final size:30
Alignment explanation
Indices: 46323--46385 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
46313 ATATATATAT
46323 ATATATATTATTTTTACCTTAAATTATAAA
1 ATATATATTATTTTTACCTTAAATTATAAA
* * *
46353 ATATATTTTATTTTTACTTTAACTTA-AAA
1 ATATATATTATTTTTACCTTAAATTATAAA
46382 ATAT
1 ATAT
46386 TTTAATCTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 7 0.23
30 23 0.77
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.52
Consensus pattern (30 bp):
ATATATATTATTTTTACCTTAAATTATAAA
Found at i:46400 original size:27 final size:27
Alignment explanation
Indices: 46349--46417 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 27
46339 CCTTAAATTA
* *
46349 TAAAATATATTTTATTTTTACTTTAACT
1 TAAAA-ATATTTTAATCTTACTTTAACT
* *
46377 TAAAAATATTTTAATCTTATTTTAAGT
1 TAAAAATATTTTAATCTTACTTTAACT
* *
46404 TAAAATTAATTTAA
1 TAAAAATATTTTAA
46418 GATAAAATAT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
27 30 0.86
28 5 0.14
ACGTcount: A:0.42, C:0.04, G:0.01, T:0.52
Consensus pattern (27 bp):
TAAAAATATTTTAATCTTACTTTAACT
Found at i:46416 original size:16 final size:17
Alignment explanation
Indices: 46397--46430 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
46387 TTAATCTTAT
*
46397 TTTAAGTTAAAAT-TAA
1 TTTAAGATAAAATATAA
46413 TTTAAGATAAAATATAA
1 TTTAAGATAAAATATAA
46430 T
1 T
46431 ATATATATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (17 bp):
TTTAAGATAAAATATAA
Found at i:46466 original size:16 final size:17
Alignment explanation
Indices: 46445--46477 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
46435 ATATAATTAT
46445 TAAAAAT-ATAAATGTA
1 TAAAAATAATAAATGTA
46461 TAAAAATAATAAATGTA
1 TAAAAATAATAAATGTA
46478 ATTTTAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (17 bp):
TAAAAATAATAAATGTA
Found at i:46488 original size:36 final size:41
Alignment explanation
Indices: 46419--46492 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 41
46409 TTAATTTAAG
46419 ATAAAATATAATATATATATAATTATTAAAAATATAAATGT
1 ATAAAATATAATATATATATAATTATTAAAAATATAAATGT
*
46460 ATAAAA-ATAATA-A-ATGTAATT-TT-AAAATATAAA
1 ATAAAATATAATATATATATAATTATTAAAAATATAAA
46493 AATCTTAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
36 10 0.31
37 2 0.06
38 7 0.22
39 1 0.03
40 6 0.19
41 6 0.19
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (41 bp):
ATAAAATATAATATATATATAATTATTAAAAATATAAATGT
Found at i:46501 original size:28 final size:29
Alignment explanation
Indices: 46459--46519 Score: 72
Period size: 28 Copynumber: 2.1 Consensus size: 29
46449 AATATAAATG
46459 TATAAAAATAAT-AAATGTA-ATTTTAAAA
1 TATAAAAATAATAAAAT-TATATTTTAAAA
**
46487 TATAAAAATCTTAAAATTATTATTTTAAAA
1 TATAAAAATAATAAAATTA-TATTTTAAAA
46517 TAT
1 TAT
46520 TATATTAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 12 0.43
29 4 0.14
30 12 0.43
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (29 bp):
TATAAAAATAATAAAATTATATTTTAAAA
Found at i:46589 original size:15 final size:15
Alignment explanation
Indices: 46569--46621 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
46559 AATTATAAAT
*
46569 TATATAGTAGAAGGA
1 TATATAATAGAAGGA
46584 TATATAATAGAAGGA
1 TATATAATAGAAGGA
* *
46599 TGTGATAATTA-AATGA
1 TAT-ATAA-TAGAAGGA
46615 TATATAA
1 TATATAA
46622 GGAAAGATGT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
15 20 0.62
16 10 0.31
17 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.19, T:0.32
Consensus pattern (15 bp):
TATATAATAGAAGGA
Found at i:47242 original size:21 final size:21
Alignment explanation
Indices: 47218--47266 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
47208 TAAAGTCTCG
47218 AGTCAAGCTCAAATCAACCCA
1 AGTCAAGCTCAAATCAACCCA
*
47239 AGTCGAGCTCAAATCAACCCA
1 AGTCAAGCTCAAATCAACCCA
47260 AGTCAAG
1 AGTCAAG
47267 TTTTTACCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.41, C:0.31, G:0.14, T:0.14
Consensus pattern (21 bp):
AGTCAAGCTCAAATCAACCCA
Found at i:53171 original size:35 final size:35
Alignment explanation
Indices: 53132--53200 Score: 102
Period size: 35 Copynumber: 2.0 Consensus size: 35
53122 TTCATGTTCA
53132 AAATTCCAAAACACTTCAATTACATTATAAACCCG
1 AAATTCCAAAACACTTCAATTACATTATAAACCCG
* * * *
53167 AAATTCCAAAATACTTTAATTATATTTTAAACCC
1 AAATTCCAAAACACTTCAATTACATTATAAACCC
53201 TAAAATAAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.45, C:0.22, G:0.01, T:0.32
Consensus pattern (35 bp):
AAATTCCAAAACACTTCAATTACATTATAAACCCG
Found at i:53276 original size:34 final size:35
Alignment explanation
Indices: 53211--53278 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 35
53201 TAAAATAAAG
*
53211 TATTTTAGAATTTAAGGTTTAAAATGTAATTGAAT
1 TATTTTAGAATTTAAGGTTTAAAATGAAATTGAAT
* * *
53246 TATTTTGGAATTT-GGGTTTAGAATGAAATTGAA
1 TATTTTAGAATTTAAGGTTTAAAATGAAATTGAA
53279 GATTGTGTTG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.37, C:0.00, G:0.19, T:0.44
Consensus pattern (35 bp):
TATTTTAGAATTTAAGGTTTAAAATGAAATTGAAT
Found at i:54171 original size:53 final size:57
Alignment explanation
Indices: 54111--54217 Score: 134
Period size: 58 Copynumber: 1.9 Consensus size: 57
54101 AATAGTATTG
* *
54111 AAATATTATT-TTCTA-TAA-T-TTTA-GAATATAAATATTTTATTTTATTAAATAAT
1 AAATATTATTATTATATTAATTATTTATGAATATAAA-ATTTTATATTATTAAATAAT
*
54164 AAATATTATTAATTATATTAATTATTTATTAATATAAAATTTTATATTATTAAA
1 AAATATTATT-ATTATATTAATTATTTATGAATATAAAATTTTATATTATTAAA
54218 AGTATTTTAA
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
53 10 0.22
55 4 0.09
56 3 0.07
57 1 0.02
58 19 0.42
59 8 0.18
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (57 bp):
AAATATTATTATTATATTAATTATTTATGAATATAAAATTTTATATTATTAAATAAT
Found at i:54724 original size:35 final size:37
Alignment explanation
Indices: 54657--54725 Score: 88
Period size: 36 Copynumber: 1.9 Consensus size: 37
54647 GAAAATATTT
* * *
54657 ATATATTTTGTTTAAAAAATTTAAATTCATAAAATTC
1 ATATACTTTGTTTAAAAAATTAAAAATCATAAAATTC
*
54694 ATATACTTT-TTTACAAAATTAAAAAT-ATAAAA
1 ATATACTTTGTTTAAAAAATTAAAAATCATAAAA
54726 AGGTTTAATG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
35 6 0.21
36 14 0.50
37 8 0.29
ACGTcount: A:0.51, C:0.06, G:0.01, T:0.42
Consensus pattern (37 bp):
ATATACTTTGTTTAAAAAATTAAAAATCATAAAATTC
Found at i:56450 original size:65 final size:64
Alignment explanation
Indices: 56317--56476 Score: 257
Period size: 65 Copynumber: 2.5 Consensus size: 64
56307 TGCACTAAGA
* * *
56317 GTGCATCGATGCATAAAATGCATTCGATGTTTTGAAAAAGCCTGAGTGCATCGATGTATGGTAT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAAACCCTGAGTGCATCGATGCATGGTAT
* * *
56381 GTGCATCGATGAATCAAATGCTTTCGATGTTTTTATAAAACCCTGAGTGCATCGATGCATGGTAT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTGA-AAAACCCTGAGTGCATCGATGCATGGTAT
56446 GTGCATCGATGCATCAAATGCATTCGATGTT
1 GTGCATCGATGCATCAAATGCATTCGATGTT
56477 CAATTAAATC
Statistics
Matches: 87, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
64 31 0.36
65 56 0.64
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.33
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAAACCCTGAGTGCATCGATGCATGGTAT
Found at i:56516 original size:65 final size:64
Alignment explanation
Indices: 56317--56524 Score: 233
Period size: 65 Copynumber: 3.2 Consensus size: 64
56307 TGCACTAAGA
* * * *
56317 GTGCATCGATGCATAAAATGCATTCGATGTTTTGAA-AAAGCCTGAGTGCATCGATGTATGGTAT
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCAATAAACCCTGAGTGCATCGATGCATGGTAT
* * **
56381 GTGCATCGATGAATCAAATGCTTTCGATGTTTTTATAAAACCCTGAGTGCATCGATGCATGGTAT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAAT-AAACCCTGAGTGCATCGATGCATGGTAT
* * * *
56446 GTGCATCGATGCATCAAATGCATTCGATG-TTCAATTAAATCATCG-GTGCATCGATGCATAGTT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAA-TAAACCCT-GAGTGCATCGATGCATGGTA
56509 T
64 T
*
56510 GATGCATCGGTGCAT
1 G-TGCATCGATGCAT
56525 GCCTTTGAAT
Statistics
Matches: 123, Mismatches: 16, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
63 4 0.03
64 52 0.42
65 67 0.54
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.32
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCAATAAACCCTGAGTGCATCGATGCATGGTAT
Found at i:62358 original size:21 final size:21
Alignment explanation
Indices: 62332--62456 Score: 96
Period size: 21 Copynumber: 5.8 Consensus size: 21
62322 AGTCGAGGTT
62332 TTATGTGGTC-CTTCGGGACAA
1 TTATGTGG-CACTTCGGGACAA
*
62353 TTATGTGGTCA-TTCGAGACAA
1 TTATGTGG-CACTTCGGGACAA
*
62374 ATATGTGGCACTTC-GGAGCAAA
1 TTATGTGGCACTTCGGGA-C-AA
* *
62396 CCTATGTGGCACTTCGGTGTAAAA
1 -TTATGTGGCACTTCGG-G-ACAA
* *
62420 CTATGTGGTC-CTTCAGGACAA
1 TTATGTGG-CACTTCGGGACAA
62441 TTATGTGGCACTTCGG
1 TTATGTGGCACTTCGG
62457 TGCAAATTAC
Statistics
Matches: 85, Mismatches: 9, Indels: 20
0.75 0.08 0.18
Matches are distributed among these distances:
20 5 0.06
21 45 0.53
22 3 0.04
23 26 0.31
24 4 0.05
25 1 0.01
26 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.30
Consensus pattern (21 bp):
TTATGTGGCACTTCGGGACAA
Found at i:65195 original size:19 final size:19
Alignment explanation
Indices: 65171--65212 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
65161 CAACCAATCA
65171 CGCCAACATCTCAAGCTAT
1 CGCCAACATCTCAAGCTAT
65190 CGCCAACATCTCAAGCTAT
1 CGCCAACATCTCAAGCTAT
65209 CGCC
1 CGCC
65213 GCTGTTGGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.29, C:0.40, G:0.12, T:0.19
Consensus pattern (19 bp):
CGCCAACATCTCAAGCTAT
Done.