Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003483.1 Hibiscus syriacus cultivar Beakdansim tig00007361_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: 71000
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:2612 original size:19 final size:19
Alignment explanation
Indices: 2575--2619 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
2565 CGAAAAAAAA
*
2575 TTATTA-TTTCTATCGATT
1 TTATTATTTTCTACCGATT
*
2593 TTATTATTTTTTACCGATT
1 TTATTATTTTCTACCGATT
2612 TTATTATT
1 TTATTATT
2620 GTTGAACACT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 6 0.25
19 18 0.75
ACGTcount: A:0.22, C:0.09, G:0.04, T:0.64
Consensus pattern (19 bp):
TTATTATTTTCTACCGATT
Found at i:2697 original size:24 final size:21
Alignment explanation
Indices: 2645--2688 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
2635 AAAACGTTAA
* *
2645 AAAAATATTAATGTTTTAAGT
1 AAAAATAATAATATTTTAAGT
2666 AAAAATAATAATATTTTAAGT
1 AAAAATAATAATATTTTAAGT
2687 AA
1 AA
2689 TTTAAATAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.39
Consensus pattern (21 bp):
AAAAATAATAATATTTTAAGT
Found at i:3800 original size:18 final size:21
Alignment explanation
Indices: 3779--3845 Score: 82
Period size: 22 Copynumber: 3.1 Consensus size: 21
3769 AAGTACAATA
3779 ATATAT-TAGGTAGCGCTTAT
1 ATATATATAGGTAGCGCTTAT
3799 ATAATATATAGGTAGCGCTTAT
1 AT-ATATATAGGTAGCGCTTAT
* *
3821 ATAATATAATAGGTAACGTTTAT
1 AT-ATAT-ATAGGTAGCGCTTAT
3844 AT
1 AT
3846 TGACCTATTT
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
20 2 0.05
21 4 0.10
22 21 0.50
23 15 0.36
ACGTcount: A:0.37, C:0.07, G:0.16, T:0.39
Consensus pattern (21 bp):
ATATATATAGGTAGCGCTTAT
Found at i:3827 original size:20 final size:22
Alignment explanation
Indices: 3776--3845 Score: 104
Period size: 23 Copynumber: 3.1 Consensus size: 22
3766 ATCAAGTACA
3776 ATAATATATTAGGTAGCGCTTAT
1 ATAATATA-TAGGTAGCGCTTAT
3799 ATAATATATAGGTAGCGCTTAT
1 ATAATATATAGGTAGCGCTTAT
* *
3821 ATAATATAATAGGTAACGTTTAT
1 ATAATAT-ATAGGTAGCGCTTAT
3844 AT
1 AT
3846 TGACCTATTT
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
22 21 0.48
23 23 0.52
ACGTcount: A:0.39, C:0.07, G:0.16, T:0.39
Consensus pattern (22 bp):
ATAATATATAGGTAGCGCTTAT
Found at i:4997 original size:111 final size:111
Alignment explanation
Indices: 4751--5104 Score: 590
Period size: 111 Copynumber: 3.2 Consensus size: 111
4741 TTCCAAAAGT
* *
4751 ATCGATAC-TTATAATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTG-TTTGTC
1 ATCGATACATTTTTATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTC
* * * *
4814 ATTATAGACCAGTTTTATCA--TTTTTACCTGTTTTATTGTTATAG
66 ATTATAGACCGGTTTTGTCATTTTTTTACCTGTTATATTGTTATGG
*
4858 ATCGATACATTTTTATAAAGTATTGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTC
1 ATCGATACATTTTTATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTC
*
4923 ATTATAGACCGGTTTTGTCATTTTTTTACCTGTTATATTATTATGG
66 ATTATAGACCGGTTTTGTCATTTTTTTACCTGTTATATTGTTATGG
4969 ATCGATACATTTTTATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTC
1 ATCGATACATTTTTATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTC
5034 ATTTATAGACCGGTTTTGTCATTTTTTTTACCTGTTATATTGTTATGG
66 A-TTATAGACCGGTTTTGTCA-TTTTTTTACCTGTTATATTGTTATGG
5082 ATCGATACATTTTTATAAAGTAT
1 ATCGATACATTTTTATAAAGTAT
5105 TGAGCGCTTT
Statistics
Matches: 231, Mismatches: 10, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
107 8 0.03
108 46 0.20
109 24 0.10
111 86 0.37
112 19 0.08
113 48 0.21
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (111 bp):
ATCGATACATTTTTATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTC
ATTATAGACCGGTTTTGTCATTTTTTTACCTGTTATATTGTTATGG
Found at i:5123 original size:93 final size:91
Alignment explanation
Indices: 5014--5195 Score: 274
Period size: 93 Copynumber: 2.0 Consensus size: 91
5004 CATATCCGGT
* ** *
5014 AGCGCTTTACCTGTTTTGTCATTTATAGACCGGTTTTGTCATTTTTTTTACCTGTTATATTGTTA
1 AGCGCTTTACCTGTTTTGTCATTTATAGACCGGTTTTGTAATTTTTTTT-CCTGCCATATTATTA
*
5079 TGGATCGATACATTTTTATAAAGTATTG
65 TGGATCAATACA-TTTTATAAAGTATTG
*
5107 AGCGCTTTACCTGTTTTGTCATTTATAGACCGGTTTTGTAATTTTTTTTCTTGCCATATTATTAT
1 AGCGCTTTACCTGTTTTGTCATTTATAGACCGGTTTTGTAATTTTTTTTCCTGCCATATTATTAT
* *
5172 GGATTAATATATTTTATAAAGTAT
66 GGATCAATACATTTTATAAAGTAT
5196 CGACAGAAAT
Statistics
Matches: 81, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
91 13 0.16
92 20 0.25
93 48 0.59
ACGTcount: A:0.23, C:0.12, G:0.15, T:0.50
Consensus pattern (91 bp):
AGCGCTTTACCTGTTTTGTCATTTATAGACCGGTTTTGTAATTTTTTTTCCTGCCATATTATTAT
GGATCAATACATTTTATAAAGTATTG
Found at i:9967 original size:34 final size:35
Alignment explanation
Indices: 9924--10004 Score: 103
Period size: 34 Copynumber: 2.4 Consensus size: 35
9914 TTTAAATATA
* * * * *
9924 TAGTTGTTTAGAAATATTTTAAAAGTAG-TATTGG
1 TAGTCGTTTAAAAATATTTGAAAAGTAGTTAATAG
9958 TAGTCGTTTAAAAATATTTGAAAAGTAGTTAATAG
1 TAGTCGTTTAAAAATATTTGAAAAGTAGTTAATAG
9993 TAGTCG-TTAAAA
1 TAGTCGTTTAAAA
10005 CTCATAGGGT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
34 31 0.76
35 10 0.24
ACGTcount: A:0.40, C:0.02, G:0.19, T:0.40
Consensus pattern (35 bp):
TAGTCGTTTAAAAATATTTGAAAAGTAGTTAATAG
Found at i:10293 original size:37 final size:36
Alignment explanation
Indices: 10223--10294 Score: 92
Period size: 37 Copynumber: 2.0 Consensus size: 36
10213 TGGAAAATAA
* *
10223 TTATATATTTTCTTTAAAAATTTAAATTCATAAAAT
1 TTATATATTTTCTTTAAAAATTGAAAATCATAAAAT
*
10259 TTATATAATTTTTTTTACAAAATTGAAAAT-ATAAAA
1 TTATAT-ATTTTCTTTA-AAAATTGAAAATCATAAAA
10295 AAGGTTTAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
36 6 0.19
37 15 0.48
38 10 0.32
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.47
Consensus pattern (36 bp):
TTATATATTTTCTTTAAAAATTGAAAATCATAAAAT
Found at i:12233 original size:18 final size:18
Alignment explanation
Indices: 12210--12248 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
12200 ATCCAATCAT
12210 TATTTTTTCGTTCGGTGC
1 TATTTTTTCGTTCGGTGC
12228 TATTTTTTCGTTCGGTGC
1 TATTTTTTCGTTCGGTGC
12246 TAT
1 TAT
12249 AAGGGGTCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.08, C:0.15, G:0.21, T:0.56
Consensus pattern (18 bp):
TATTTTTTCGTTCGGTGC
Found at i:14930 original size:3 final size:3
Alignment explanation
Indices: 14922--15024 Score: 55
Period size: 3 Copynumber: 32.0 Consensus size: 3
14912 TAGTCATTGT
* **
14922 TTA TTA TTA ATA TTA TTA TTAA TTA TTAA TGG TGT- TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TT-A TTA TT-A TTA T-TA TTA TTA TTA TTA
* * * * *
14969 GTCA TTAA TTA TTTA TTA ATA TTA TTA TCA TTTA ATA TTA CTA TTTA
1 -TTA TT-A TTA -TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA -TTA
15016 TTA TTA TTA
1 TTA TTA TTA
15025 GATAATATTA
Statistics
Matches: 76, Mismatches: 15, Indels: 18
0.70 0.14 0.17
Matches are distributed among these distances:
2 1 0.01
3 58 0.76
4 17 0.22
ACGTcount: A:0.35, C:0.03, G:0.04, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:14939 original size:12 final size:13
Alignment explanation
Indices: 14922--15024 Score: 66
Period size: 13 Copynumber: 7.7 Consensus size: 13
14912 TAGTCATTGT
14922 TTATTATTAA-TA
1 TTATTATTAATTA
14934 TTATTATTAATTA
1 TTATTATTAATTA
* *
14947 TTAATGGTGTTTATTA
1 TT-AT--TATTAATTA
* *
14963 TTATTAGTCATTAA
1 TTATTATTAATT-A
14977 TTATTTATTAA-TA
1 TTA-TTATTAATTA
* *
14990 TTATTATCATTTA
1 TTATTATTAATTA
* * *
15003 ATATTACTATTTA
1 TTATTATTAATTA
15016 TTATTATTA
1 TTATTATTA
15025 GATAATATTA
Statistics
Matches: 70, Mismatches: 14, Indels: 13
0.72 0.14 0.13
Matches are distributed among these distances:
12 15 0.21
13 32 0.46
14 7 0.10
15 7 0.10
16 9 0.13
ACGTcount: A:0.35, C:0.03, G:0.04, T:0.58
Consensus pattern (13 bp):
TTATTATTAATTA
Found at i:14939 original size:26 final size:26
Alignment explanation
Indices: 14908--15000 Score: 80
Period size: 26 Copynumber: 3.5 Consensus size: 26
14898 TTTGTCCAGG
*
14908 TTATTAGTCATTGTTTATTATTAATA
1 TTATTAGTCATTATTTATTATTAATA
* * * * *
14934 TTATTATTAATTATTAATGGTGTTTATTA
1 TTATTAGTCATTATTTAT--T-ATTAATA
*
14963 TTATTAGTCATTAATTATTTATTAATA
1 TTATTAGTCATTATTTA-TTATTAATA
14990 TTATTA-TCATT
1 TTATTAGTCATT
15001 TAATATTACT
Statistics
Matches: 51, Mismatches: 12, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
26 19 0.37
27 11 0.22
28 2 0.04
29 18 0.35
30 1 0.02
ACGTcount: A:0.32, C:0.03, G:0.06, T:0.58
Consensus pattern (26 bp):
TTATTAGTCATTATTTATTATTAATA
Found at i:15016 original size:56 final size:55
Alignment explanation
Indices: 14908--15025 Score: 146
Period size: 56 Copynumber: 2.1 Consensus size: 55
14898 TTTGTCCAGG
** * * ** *
14908 TTATTAGTCATTGTTTATTATTAATATTATTATTAATTATTAATGGTGTTTATTA
1 TTATTAGTCATTAATTATTATTAATATTATTATCAATTAATAATACTATTTATTA
* *
14963 TTATTAGTCATTAATTATTTATTAATATTATTATCATTTAATATTACTATTTATTA
1 TTATTAGTCATTAATTA-TTATTAATATTATTATCAATTAATAATACTATTTATTA
15019 TTATTAG
1 TTATTAG
15026 ATAATATTAC
Statistics
Matches: 53, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
55 15 0.28
56 38 0.72
ACGTcount: A:0.33, C:0.03, G:0.06, T:0.58
Consensus pattern (55 bp):
TTATTAGTCATTAATTATTATTAATATTATTATCAATTAATAATACTATTTATTA
Found at i:15017 original size:26 final size:26
Alignment explanation
Indices: 14988--15043 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 26
14978 TATTTATTAA
** *
14988 TATTATTATCATTTAATATTACTATT
1 TATTATTATCAGATAATATTACTAGT
*
15014 TATTATTATTAGATAATATTACTAGT
1 TATTATTATCAGATAATATTACTAGT
15040 TATT
1 TATT
15044 CATATGATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.36, C:0.05, G:0.04, T:0.55
Consensus pattern (26 bp):
TATTATTATCAGATAATATTACTAGT
Found at i:20156 original size:91 final size:90
Alignment explanation
Indices: 20001--20183 Score: 223
Period size: 91 Copynumber: 2.0 Consensus size: 90
19991 ATTTTCAAAG
*
20001 TGATGCATCGATGCACCAATCCATGCATCGATGCACCATGGAATTAATTGAACATCTAATGCATT
1 TGATGCATCGATGCACCAAACCATGCATCGATGCACCATGGAATTAA-T-AACATCTAATGCATT
*
20066 TTATGCATCGATGCA-CTTAGTGCACT
64 TCATGCATCGATGCACCTTAGTGCACT
*
20092 TGATGCATCGATGCA-CAAGACCATGCATCGATGCACTCA-GGCTATTTCAA-AACAT-TGAATG
1 TGATGCATCGATGCACCAA-ACCATGCATCGATGCAC-CATGG--AATT-AATAACATCT-AATG
20153 CATTTCATGCATCGATGCACTCTTAGTGCAC
60 CATTTCATGCATCGATGCAC-CTTAGTGCAC
20184 CGATGCACTG
Statistics
Matches: 81, Mismatches: 3, Indels: 14
0.83 0.03 0.14
Matches are distributed among these distances:
90 4 0.05
91 60 0.74
92 2 0.02
93 13 0.16
94 2 0.02
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28
Consensus pattern (90 bp):
TGATGCATCGATGCACCAAACCATGCATCGATGCACCATGGAATTAATAACATCTAATGCATTTC
ATGCATCGATGCACCTTAGTGCACT
Found at i:22168 original size:22 final size:21
Alignment explanation
Indices: 22146--22185 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
22136 AAGACTATAT
22146 TTTCAAAATAT-AAAAATGATA
1 TTTCAAAAT-TGAAAAATGATA
22167 TTTCAAAATTGAAAAATGA
1 TTTCAAAATTGAAAAATGA
22186 AAATAGTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.55, C:0.05, G:0.07, T:0.33
Consensus pattern (21 bp):
TTTCAAAATTGAAAAATGATA
Found at i:28730 original size:45 final size:46
Alignment explanation
Indices: 28681--28768 Score: 142
Period size: 45 Copynumber: 1.9 Consensus size: 46
28671 GAACATCGGA
* * *
28681 TGCATTTTATGCATCGATGCAC-ATACCATGCATCGATGCACTTAG
1 TGCATTTGATGCATCGATGAACAAGACCATGCATCGATGCACTTAG
28726 TGCATTTGATGCATCGATGAACAAGACCATGCATCGATGCACT
1 TGCATTTGATGCATCGATGAACAAGACCATGCATCGATGCACT
28769 CAGGCTATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 20 0.51
46 19 0.49
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.28
Consensus pattern (46 bp):
TGCATTTGATGCATCGATGAACAAGACCATGCATCGATGCACTTAG
Found at i:30293 original size:19 final size:18
Alignment explanation
Indices: 30271--30311 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
30261 TTCTGCTTCC
*
30271 TTTTAATTGACTATTTTG
1 TTTTTATTGACTATTTTG
*
30289 TTTTTCTTGACTATTTTG
1 TTTTTATTGACTATTTTG
30307 TTTTT
1 TTTTT
30312 CTTTGCAAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.15, C:0.07, G:0.10, T:0.68
Consensus pattern (18 bp):
TTTTTATTGACTATTTTG
Found at i:30311 original size:18 final size:18
Alignment explanation
Indices: 30277--30314 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
30267 TTCCTTTTAA
30277 TTGACTATTTTGTTTTTC
1 TTGACTATTTTGTTTTTC
30295 TTGACTATTTTGTTTTTC
1 TTGACTATTTTGTTTTTC
30313 TT
1 TT
30315 TGCAAGGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.11, C:0.11, G:0.11, T:0.68
Consensus pattern (18 bp):
TTGACTATTTTGTTTTTC
Found at i:30846 original size:10 final size:10
Alignment explanation
Indices: 30831--30863 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
30821 AAACCCCACT
30831 AAAAATGAAA
1 AAAAATGAAA
30841 AAAAATGAAA
1 AAAAATGAAA
*
30851 AAAATTGAAA
1 AAAAATGAAA
30861 AAA
1 AAA
30864 TGAAGTTGTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.79, C:0.00, G:0.09, T:0.12
Consensus pattern (10 bp):
AAAAATGAAA
Found at i:31395 original size:10 final size:10
Alignment explanation
Indices: 31363--31419 Score: 71
Period size: 10 Copynumber: 5.7 Consensus size: 10
31353 TCTAATAGCT
31363 CATTTAGGAA-
1 CATTTA-GAAG
* *
31373 CATATAGATG
1 CATTTAGAAG
31383 CATTTAGAAG
1 CATTTAGAAG
*
31393 CATTTAGATG
1 CATTTAGAAG
31403 CATTTAGAAG
1 CATTTAGAAG
31413 CATTTAG
1 CATTTAG
31420 TTGCATGCGG
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
9 2 0.05
10 38 0.95
ACGTcount: A:0.37, C:0.11, G:0.19, T:0.33
Consensus pattern (10 bp):
CATTTAGAAG
Found at i:31425 original size:10 final size:10
Alignment explanation
Indices: 31377--31425 Score: 71
Period size: 10 Copynumber: 4.9 Consensus size: 10
31367 TAGGAACATA
31377 TAGATGCATT
1 TAGATGCATT
*
31387 TAGAAGCATT
1 TAGATGCATT
31397 TAGATGCATT
1 TAGATGCATT
*
31407 TAGAAGCATT
1 TAGATGCATT
*
31417 TAGTTGCAT
1 TAGATGCAT
31426 GCGGTGCTGC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
10 34 1.00
ACGTcount: A:0.33, C:0.10, G:0.20, T:0.37
Consensus pattern (10 bp):
TAGATGCATT
Found at i:40230 original size:31 final size:31
Alignment explanation
Indices: 40185--40252 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
40175 CGTTTATGTT
* * *
40185 AAGTGGCAATGTCTTAATTAAAATGAAATAA
1 AAGTGACAACGTCTTAATTAAAATGAAACAA
*
40216 AAGTGACAACGTCTTAATTAAATTGAAACAA
1 AAGTGACAACGTCTTAATTAAAATGAAACAA
40247 AAGTGA
1 AAGTGA
40253 TCAAATATTA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.49, C:0.09, G:0.16, T:0.26
Consensus pattern (31 bp):
AAGTGACAACGTCTTAATTAAAATGAAACAA
Found at i:40264 original size:31 final size:31
Alignment explanation
Indices: 40198--40265 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
40188 TGGCAATGTC
* * *
40198 TTAATTAAAATGAAATAAAAGTGACAACGTC
1 TTAATTAAAATGAAACAAAAGTGACAACATA
*
40229 TTAATTAAATTGAAACAAAAGTGATCAA-ATA
1 TTAATTAAAATGAAACAAAAGTGA-CAACATA
40260 TTAATT
1 TTAATT
40266 TTTTTTGATC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 29 0.91
32 3 0.09
ACGTcount: A:0.51, C:0.07, G:0.10, T:0.31
Consensus pattern (31 bp):
TTAATTAAAATGAAACAAAAGTGACAACATA
Found at i:56607 original size:24 final size:26
Alignment explanation
Indices: 56569--56616 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
56559 ACTCGAACTT
56569 AAAAATTAATCTA-T-TAATTATTAA
1 AAAAATTAATCTATTCTAATTATTAA
56593 AAAAATTAAAT-TATTCTAATTATT
1 AAAAATT-AATCTATTCTAATTATT
56617 GGAGTCTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 9 0.43
25 4 0.19
26 8 0.38
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (26 bp):
AAAAATTAATCTATTCTAATTATTAA
Found at i:57594 original size:22 final size:23
Alignment explanation
Indices: 57547--57594 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
57537 TGTTCTCCAT
57547 AATTAAACCTTTCTGGGTATTCA
1 AATTAAACCTTTCTGGGTATTCA
*
57570 AATTAAACCTTTCT-GGTTTTCA
1 AATTAAACCTTTCTGGGTATTCA
57592 AAT
1 AAT
57595 ATTCGGAAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 10 0.42
23 14 0.58
ACGTcount: A:0.31, C:0.17, G:0.10, T:0.42
Consensus pattern (23 bp):
AATTAAACCTTTCTGGGTATTCA
Found at i:63301 original size:18 final size:18
Alignment explanation
Indices: 63278--63315 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
63268 TTGATTACAA
63278 TTTATCAAATCAAATAAC
1 TTTATCAAATCAAATAAC
63296 TTTATCAAATCAAATAAC
1 TTTATCAAATCAAATAAC
63314 TT
1 TT
63316 GATGGGGGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.37
Consensus pattern (18 bp):
TTTATCAAATCAAATAAC
Found at i:69491 original size:22 final size:20
Alignment explanation
Indices: 69445--69492 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
69435 TAAGATAGGG
*
69445 TTTAGGATTAGGGTTTATGG
1 TTTAGGATTAGGGTTTATGA
* *
69465 GTTAGAGATTATGGTATTATGA
1 TTTAG-GATTAGGGT-TTATGA
69487 TTTAGG
1 TTTAGG
69493 GTTTAAGATT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
20 4 0.18
21 9 0.41
22 9 0.41
ACGTcount: A:0.25, C:0.00, G:0.31, T:0.44
Consensus pattern (20 bp):
TTTAGGATTAGGGTTTATGA
Found at i:69511 original size:21 final size:19
Alignment explanation
Indices: 69487--69526 Score: 62
Period size: 21 Copynumber: 2.0 Consensus size: 19
69477 GGTATTATGA
69487 TTTAGGGTTTAAGATTTATAG
1 TTTAGGGTTTAA-A-TTATAG
69508 TTTAGGGTTTAAATTATAG
1 TTTAGGGTTTAAATTATAG
69527 GTAGCGTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.32
20 1 0.05
21 12 0.63
ACGTcount: A:0.30, C:0.00, G:0.23, T:0.47
Consensus pattern (19 bp):
TTTAGGGTTTAAATTATAG
Found at i:70581 original size:263 final size:263
Alignment explanation
Indices: 70114--70639 Score: 1025
Period size: 263 Copynumber: 2.0 Consensus size: 263
70104 GATGTCATAG
70114 CCCTGAATCAGAATGATCTTATGATCTCTTCCTCTCCAATGGAGGAAGATGTTGCACCAACTGAT
1 CCCTGAATCAGAATGATCTTATGATCTCTTCCTCTCCAATGGAGGAAGATGTTGCACCAACTGAT
*
70179 CCCGCTTTCCAAATGAATCTGGACACCGCTCAACCAGTGAAGTCTTATGCTGAGACGATAGCAGG
66 CCCGCTTTCCAAATGAATCTAGACACCGCTCAACCAGTGAAGTCTTATGCTGAGACGATAGCAGG
70244 TTCATCTGGACTTCCACAATCTGTCATCCCGATTTTTGGTGATAATGATGTTAAAATTCAGGAAG
131 TTCATCTGGACTTCCACAATCTGTCATCCCGATTTTTGGTGATAATGATGTTAAAATTCAGGAAG
70309 GCGACTTTACTGTGAATCGTAGTGGTCCCTATCCAATTGTCAATTTTTCTGATCATGTGCATGAT
196 GCGACTTTACTGTGAATCGTAGTGGTCCCTATCCAATTGTCAATTTTTCTGATCATGTGCATGAT
70374 TAA
261 TAA
70377 CCCTGAATCAGAATGATCTTATGATCTCTTCCTCTCCAATGGAGGAAGATGTTGCACCAACTGAT
1 CCCTGAATCAGAATGATCTTATGATCTCTTCCTCTCCAATGGAGGAAGATGTTGCACCAACTGAT
70442 CCCGCTTTCCAAATGAATCTAGACACCGCTCAACCAGTGAAGTCTTATGCTGAGACGATAGCAGG
66 CCCGCTTTCCAAATGAATCTAGACACCGCTCAACCAGTGAAGTCTTATGCTGAGACGATAGCAGG
*
70507 TTCATCTGGACTTCCACAATCTGTCATCCCGATTTTTGGTGATAATGATGTTACAATTCAGGAAG
131 TTCATCTGGACTTCCACAATCTGTCATCCCGATTTTTGGTGATAATGATGTTAAAATTCAGGAAG
*
70572 GCGACTTTACTGTGAATCGTAGTGGTTCCTATCCAATTGTCAATTTTTCTGATCATGTGCATGAT
196 GCGACTTTACTGTGAATCGTAGTGGTCCCTATCCAATTGTCAATTTTTCTGATCATGTGCATGAT
70637 TAA
261 TAA
70640 TCCATTGACC
Statistics
Matches: 260, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
263 260 1.00
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (263 bp):
CCCTGAATCAGAATGATCTTATGATCTCTTCCTCTCCAATGGAGGAAGATGTTGCACCAACTGAT
CCCGCTTTCCAAATGAATCTAGACACCGCTCAACCAGTGAAGTCTTATGCTGAGACGATAGCAGG
TTCATCTGGACTTCCACAATCTGTCATCCCGATTTTTGGTGATAATGATGTTAAAATTCAGGAAG
GCGACTTTACTGTGAATCGTAGTGGTCCCTATCCAATTGTCAATTTTTCTGATCATGTGCATGAT
TAA
Done.