Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002721.1 Hibiscus syriacus cultivar Beakdansim tig00005613_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: 50361
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:3094 original size:21 final size:21
Alignment explanation
Indices: 3068--3107 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3058 CCCCCTTTGA
*
3068 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
3089 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
3108 TGGGGTTCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:10435 original size:20 final size:21
Alignment explanation
Indices: 10412--10450 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
10402 TTATAATTAA
*
10412 TTTTTATA-AATAACTAAACT
1 TTTTTATAGAATAAATAAACT
10432 TTTTTATAGAATAAATAAA
1 TTTTTATAGAATAAATAAA
10451 TAATTAAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.44
Consensus pattern (21 bp):
TTTTTATAGAATAAATAAACT
Found at i:12768 original size:23 final size:21
Alignment explanation
Indices: 12735--12792 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 21
12725 ATTACAATGT
*
12735 TAATATTTTAAAAAGTGATCTTAA
1 TAAT-TTTTAAAAA-TGATATT-A
12759 TAATTTTTAAAAATGATATTA
1 TAATTTTTAAAAATGATATTA
12780 -AATTTATTAAAAA
1 TAATTT-TTAAAAA
12793 AATTAAAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
20 5 0.16
21 8 0.25
22 6 0.19
23 9 0.28
24 4 0.12
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (21 bp):
TAATTTTTAAAAATGATATTA
Found at i:12770 original size:22 final size:21
Alignment explanation
Indices: 12734--12793 Score: 59
Period size: 22 Copynumber: 2.8 Consensus size: 21
12724 AATTACAATG
* *
12734 TTAATATTTTAAAAAGTGATC
1 TTAATATTTTAAAAAATGATA
*
12755 TTAATAATTTTTAAAAATGATA
1 TTAAT-ATTTTAAAAAATGATA
12777 TTAA-ATTTATTAAAAAA
1 TTAATA-TT-TTAAAAAA
12794 ATTAAAATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
20 1 0.03
21 7 0.22
22 24 0.75
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (21 bp):
TTAATATTTTAAAAAATGATA
Found at i:13227 original size:37 final size:37
Alignment explanation
Indices: 13181--13292 Score: 188
Period size: 37 Copynumber: 3.0 Consensus size: 37
13171 AACATAACGT
*
13181 TAGAGTTTTACTAAGATTCAAACTCCTAAAAATAGGA
1 TAGAGTTTTACTATGATTCAAACTCCTAAAAATAGGA
* *
13218 TAGATTTTTACTATGATTTAAACTCCTAAAAATAGGA
1 TAGAGTTTTACTATGATTCAAACTCCTAAAAATAGGA
*
13255 TAGAGTTCTACTATGATTCAAACTCCTAAAAATAGGA
1 TAGAGTTTTACTATGATTCAAACTCCTAAAAATAGGA
13292 T
1 T
13293 CCACAAGCGT
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 69 1.00
ACGTcount: A:0.41, C:0.13, G:0.12, T:0.33
Consensus pattern (37 bp):
TAGAGTTTTACTATGATTCAAACTCCTAAAAATAGGA
Found at i:13748 original size:22 final size:22
Alignment explanation
Indices: 13689--13751 Score: 63
Period size: 23 Copynumber: 2.8 Consensus size: 22
13679 CATGTAATGT
* ** *
13689 TTTTTAGATTTTATGCATTTTC
1 TTTTTAGATTATATATATTTTA
**
13711 TTTTTACTTTAGTATATATTTTA
1 TTTTTAGATTA-TATATATTTTA
13734 TTTTTAGATTATATATAT
1 TTTTTAGATTATATATAT
13752 ATATATATAT
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
22 15 0.47
23 17 0.53
ACGTcount: A:0.25, C:0.05, G:0.06, T:0.63
Consensus pattern (22 bp):
TTTTTAGATTATATATATTTTA
Found at i:13919 original size:37 final size:36
Alignment explanation
Indices: 13872--13946 Score: 89
Period size: 35 Copynumber: 2.1 Consensus size: 36
13862 TTTATTATTA
*
13872 TTTTATTTATTTGTTTTATTTATAAATTTTT-TCTTAC
1 TTTTATTTA-TT-TTTTATATATAAATTTTTATCTTAC
* * *
13909 TTTTCTTTATTTTTTATATATATATTTTTATTTTAC
1 TTTTATTTATTTTTTATATATAAATTTTTATCTTAC
13945 TT
1 TT
13947 ACTATTTTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
35 16 0.48
36 9 0.27
37 8 0.24
ACGTcount: A:0.21, C:0.05, G:0.01, T:0.72
Consensus pattern (36 bp):
TTTTATTTATTTTTTATATATAAATTTTTATCTTAC
Found at i:18038 original size:32 final size:32
Alignment explanation
Indices: 18016--18103 Score: 149
Period size: 32 Copynumber: 2.8 Consensus size: 32
18006 ACCTTTGAAG
18016 ATTCAACATCAAATGTTGGGGCATTTTTGGAA
1 ATTCAACATCAAATGTTGGGGCATTTTTGGAA
18048 ATTCAACATCAAATGTTGGGGCATTTTTGGAA
1 ATTCAACATCAAATGTTGGGGCATTTTTGGAA
* * *
18080 ATGCAACATCGAATATTGGGGCAT
1 ATTCAACATCAAATGTTGGGGCAT
18104 CTTCGGGGAT
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 53 1.00
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.32
Consensus pattern (32 bp):
ATTCAACATCAAATGTTGGGGCATTTTTGGAA
Found at i:18943 original size:110 final size:110
Alignment explanation
Indices: 18639--18926 Score: 486
Period size: 110 Copynumber: 2.6 Consensus size: 110
18629 TCGAGAAAAG
*
18639 CTGACTATCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATA
1 CTGACTATCAACAAATAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATA
18704 TTGGACTCGAGACAACACAAGCTCAACTGCACAGCAAAAGGGCGA
66 TTGGACTCGAGACAACACAAGCTCAACTGCACAGCAAAAGGGCGA
* * *
18749 CTGGCTATCAACAAATAACTTTTCAGTTTTATTCAGAGTCAATTTTAACTTCACAGCGAAGGATA
1 CTGACTATCAACAAATAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATA
* * * *
18814 TAGGACTCGAGATAACACAAGCTCAACTTCACAGCGAAAGGGCGA
66 TTGGACTCGAGACAACACAAGCTCAACTGCACAGCAAAAGGGCGA
* *
18859 CTGACTGTCAACAAATAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAGTGAAGGATA
1 CTGACTATCAACAAATAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATA
18924 TTG
66 TTG
18927 AACTTGAAGC
Statistics
Matches: 164, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
110 164 1.00
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (110 bp):
CTGACTATCAACAAATAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATA
TTGGACTCGAGACAACACAAGCTCAACTGCACAGCAAAAGGGCGA
Found at i:20085 original size:37 final size:37
Alignment explanation
Indices: 20044--20192 Score: 262
Period size: 37 Copynumber: 4.0 Consensus size: 37
20034 AACATAACAT
*
20044 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATATGA
1 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
*
20081 TAGAGTTTTACTATGATTCAAACTCCTAAAAATAGGA
1 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
20118 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
1 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
* *
20155 TAGAGTTCTACTATGATTCAAACTCCTAAAAATAGGA
1 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
20192 T
1 T
20193 CCACAAGCGT
Statistics
Matches: 107, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 107 1.00
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.32
Consensus pattern (37 bp):
TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
Found at i:20716 original size:24 final size:23
Alignment explanation
Indices: 20689--20738 Score: 57
Period size: 25 Copynumber: 2.1 Consensus size: 23
20679 CATTTTATGC
*
20689 ATTTTCTTTTTTACT-TTAGTATAT
1 ATTTTATTTTTTA-TATTA-TATAT
20713 ATTTTTATTTTTTATATTATATAT
1 A-TTTTATTTTTTATATTATATAT
20737 AT
1 AT
20739 ATATATATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
23 1 0.04
24 8 0.35
25 14 0.61
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.68
Consensus pattern (23 bp):
ATTTTATTTTTTATATTATATAT
Found at i:20735 original size:2 final size:2
Alignment explanation
Indices: 20725--20836 Score: 217
Period size: 2 Copynumber: 56.5 Consensus size: 2
20715 TTTTATTTTT
20725 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
20766 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
20808 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
20837 GTGTGTGTGT
Statistics
Matches: 109, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 108 0.99
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:21101 original size:29 final size:25
Alignment explanation
Indices: 21044--21099 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
21034 TTATCTTACC
21044 TTTT-ATTTAATTTGTTTTTCTTCA
1 TTTTAATTTAATTTGTTTTTCTTCA
*
21068 TTTTAATTTAATTTATTTATTTCTTACA
1 TTTTAATTTAATTT-GTT-TTTCTT-CA
21096 TTTT
1 TTTT
21100 TATCTAACAC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
24 4 0.15
25 9 0.33
26 2 0.07
27 6 0.22
28 6 0.22
ACGTcount: A:0.21, C:0.07, G:0.02, T:0.70
Consensus pattern (25 bp):
TTTTAATTTAATTTGTTTTTCTTCA
Found at i:24676 original size:2 final size:2
Alignment explanation
Indices: 24671--24700 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
24661 TTTGTGTGTC
24671 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
24701 GAGTTTAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:25814 original size:19 final size:19
Alignment explanation
Indices: 25790--25829 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
25780 AGCACCGCAT
25790 AGCCTTCCCCCTCATCCGA
1 AGCCTTCCCCCTCATCCGA
25809 AGCCTTCCCCCTCATCCGA
1 AGCCTTCCCCCTCATCCGA
25828 AG
1 AG
25830 ACTCCTCGCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.17, C:0.50, G:0.12, T:0.20
Consensus pattern (19 bp):
AGCCTTCCCCCTCATCCGA
Found at i:25882 original size:21 final size:22
Alignment explanation
Indices: 25858--25901 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
25848 AACTCACAGC
25858 CGTGATTCTCGACA-CAACAAA
1 CGTGATTCTCGACACCAACAAA
* * *
25879 CGTGGTTTTTGACACCAACAAA
1 CGTGATTCTCGACACCAACAAA
25901 C
1 C
25902 AATAATAAAC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.23
Consensus pattern (22 bp):
CGTGATTCTCGACACCAACAAA
Found at i:27544 original size:21 final size:21
Alignment explanation
Indices: 27488--27544 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
27478 GGGAGCGTCA
* *
27488 GTGCATCGATGCATACCCATG
1 GTGCATCGGTGCATCCCCATG
27509 GTGCATCGGTGCATCCCCATG
1 GTGCATCGGTGCATCCCCATG
27530 GTGCATCGGTGCATC
1 GTGCATCGGTGCATC
27545 AGTGTAAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.18, C:0.30, G:0.28, T:0.25
Consensus pattern (21 bp):
GTGCATCGGTGCATCCCCATG
Found at i:27695 original size:26 final size:26
Alignment explanation
Indices: 27665--27736 Score: 135
Period size: 26 Copynumber: 2.8 Consensus size: 26
27655 TGCATGGTTT
27665 GTGCATCGATGCATCAAATGCACTGA
1 GTGCATCGATGCATCAAATGCACTGA
27691 GTGCATCGATGCATCAAATGCACTGA
1 GTGCATCGATGCATCAAATGCACTGA
*
27717 GTGCATCGATGCATAAAATG
1 GTGCATCGATGCATCAAATG
27737 TATTCGATGT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 45 1.00
ACGTcount: A:0.32, C:0.21, G:0.24, T:0.24
Consensus pattern (26 bp):
GTGCATCGATGCATCAAATGCACTGA
Found at i:30207 original size:23 final size:22
Alignment explanation
Indices: 30177--30278 Score: 116
Period size: 23 Copynumber: 4.6 Consensus size: 22
30167 CATGGCCTTG
30177 TGCATCGATGCACATTCAAGGCA
1 TGCATCGATGCACATTCAAGG-A
*
30200 TGCATCGATGCACATTCAAGGCG
1 TGCATCGATGCACATTCAAGG-A
* * *
30223 TGCATCGGTGCACCTTCATGG-
1 TGCATCGATGCACATTCAAGGA
*
30244 TGTATCGATGCACATTCAAGGA
1 TGCATCGATGCACATTCAAGGA
* *
30266 TACATCGGTGCAC
1 TGCATCGATGCAC
30279 TGTTAGGTGT
Statistics
Matches: 67, Mismatches: 11, Indels: 3
0.83 0.14 0.04
Matches are distributed among these distances:
21 17 0.25
22 10 0.15
23 40 0.60
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.25
Consensus pattern (22 bp):
TGCATCGATGCACATTCAAGGA
Found at i:30259 original size:44 final size:42
Alignment explanation
Indices: 30176--30297 Score: 129
Period size: 44 Copynumber: 2.8 Consensus size: 42
30166 GCATGGCCTT
* * *
30176 GTGCATCGATGCACATTCAAGGCATGCATCGATGCACATTCAAGG
1 GTGCATCGGTGCACCTTC-AGG--TGTATCGATGCACATTCAAGG
30221 CGTGCATCGGTGCACCTTCATGGTGTATCGATGCACATTCAAGG
1 -GTGCATCGGTGCACCTTCA-GGTGTATCGATGCACATTCAAGG
* * *
30265 ATACATCGGTGCA-CTGTTAGGTGTATCGATGCA
1 GTGCATCGGTGCACCT-TCAGGTGTATCGATGCA
30298 TTAAGCACAA
Statistics
Matches: 68, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
42 16 0.24
43 13 0.19
44 20 0.29
45 1 0.01
46 18 0.26
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.26
Consensus pattern (42 bp):
GTGCATCGGTGCACCTTCAGGTGTATCGATGCACATTCAAGG
Found at i:36238 original size:4 final size:4
Alignment explanation
Indices: 36224--36280 Score: 51
Period size: 4 Copynumber: 13.8 Consensus size: 4
36214 CCTTTACATT
* * * * *
36224 TTTA GTTA TTTA TTTA TTATA TATA TATA TATA TATA TATTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TT-TA TTTA TTTA TTTA TTTA T-TTA TTTA TTTA
36274 TTTA TTT
1 TTTA TTT
36281 TTAATTTTAA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
4 41 0.87
5 6 0.13
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (4 bp):
TTTA
Found at i:40243 original size:34 final size:34
Alignment explanation
Indices: 40205--40308 Score: 81
Period size: 34 Copynumber: 3.2 Consensus size: 34
40195 GAGTACATTT
40205 CAACTTCACAACGAATGATATTGGACTCAACAAA
1 CAACTTCACAACGAATGATATTGGACTCAACAAA
* * ** * ** * * *
40239 CAACTT-TCTA-GTTTCAT-TCAGAGTCAA-TAT
1 CAACTTCACAACGAATGATATTGGACTCAACAAA
*
40269 CAACTTCACAACGAAGGATATTGGACTCAACAAA
1 CAACTTCACAACGAATGATATTGGACTCAACAAA
40303 CAACTT
1 CAACTT
40309 TTCAGTTTTA
Statistics
Matches: 45, Mismatches: 21, Indels: 8
0.61 0.28 0.11
Matches are distributed among these distances:
30 7 0.16
31 9 0.20
32 7 0.16
33 9 0.20
34 13 0.29
ACGTcount: A:0.39, C:0.23, G:0.12, T:0.26
Consensus pattern (34 bp):
CAACTTCACAACGAATGATATTGGACTCAACAAA
Found at i:40289 original size:64 final size:64
Alignment explanation
Indices: 40129--40551 Score: 641
Period size: 64 Copynumber: 6.6 Consensus size: 64
40119 TGCATATTTT
* *
40129 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAAAAAATGTTCCAGTTTCATTC
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACT-TTCCAGTTTCATTC
* *
40194 AGAGT-ACATTTCAACTTCACAACGAATGATATTGGACTCAACAAACAACTTTCTAGTTTCATTC
1 AGAGTCA-ATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTC
* * *
40258 AGAGTCAATATCAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTTCAGTTTTATTC
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTC
* * * *
40322 AGAGTTAATTTTAACTTCACATCGAAGGATATTGGACTCAACAAATAACTTTCCAGTTTCATTC
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTC
* * * *
40386 AGAGTCAATTTTAACTTCACAGCGGAGGATATTGGACTCAACAAATAACTTTCCAGTTTCATTC
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTC
* **
40450 AGAGTTAATTTCAACTTCACAGTGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTC
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTC
* *
40514 AGAGTAAATTTCAACTTCACAACGAGGGATATTGGACT
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACT
40552 TGAAACAATG
Statistics
Matches: 328, Mismatches: 28, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
64 282 0.86
65 46 0.14
ACGTcount: A:0.36, C:0.20, G:0.14, T:0.30
Consensus pattern (64 bp):
AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTC
Found at i:41080 original size:309 final size:309
Alignment explanation
Indices: 40521--41162 Score: 953
Period size: 309 Copynumber: 2.1 Consensus size: 309
40511 TTCAGAGTAA
* * * *
40521 ATTTCAACTTCACAACGAGGGATATTGGACTTGAAACAATGCAACTTACACAAGATTGGATTTTA
1 ATTTCAACTTCACAACGAAGGATACTGGACTCGAAACAATGCAACTTACACAAGATTGGATTTCA
* *
40586 AATTCACGATAAAGGATAACAAACTCAAAACCAATTTGGTGAAACAACCCTTGGATTTCAATTTC
66 AATTCACGACAAAGGATAACAAACTCAAAACCAATTTGGTGAAACAACCCTTGGATTTCAACTTC
* * * *
40651 ACAACGAAGGATATCTAATTCAAAGCTCAACTTCACAACGAAGGAGCCATCCACGATTTCAACTT
131 ACAACGAAGGATATCCAATTCAAAGCTCAACTTCACAACAAAAGAGCCATCAACGATTTCAACTT
* *
40716 CACGACGAAGGATATCATACCCACAAGCAGCATCCATCTCTAGATTGGATTTCAACTTTACAACG
196 CACGAAGAAGGATATCATACCCACAAGCAGCATCCATCTCTAGATTGGATTTCAACTTCACAACG
*
40781 AAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCATCCATG
261 AAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCATCCACG
* * * *
40830 ATTTCAACTTCACATCGAATGATACTGGACTCGAAACAATGCAACTTATATAAGATTGGATTTCA
1 ATTTCAACTTCACAACGAAGGATACTGGACTCGAAACAATGCAACTTACACAAGATTGGATTTCA
* * * *
40895 ACTTCACGACGAAGGATATCCAAA-TCAAAACCAATTTGGTGAAACAACCCTTGTATTTCAACTT
66 AATTCACGACAAAGGATA-ACAAACTCAAAACCAATTTGGTGAAACAACCCTTGGATTTCAACTT
* *
40959 CACAACGAAGGATATCCAATTCAAAGCTCAACTTCACAATAAAAGAGCCATCAATGATTTCAACT
130 CACAACGAAGGATATCCAATTCAAAGCTCAACTTCACAACAAAAGAGCCATCAACGATTTCAACT
* * * * * *
41024 TCACGAAGAATGATATCTTTCCCATAAGGAGCATCCATCTCTAGATTGGATTTCAACTTCATAAC
195 TCACGAAGAAGGATATCATACCCACAAGCAGCATCCATCTCTAGATTGGATTTCAACTTCACAAC
* ** *
41089 GAATGATATCCAATTCAAAGCTCAACTTCATGACGAATGAGCTATCCACG
260 GAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCATCCACG
* *
41139 ATTTCAACTTCACGATGAAGGATA
1 ATTTCAACTTCACAACGAAGGATA
41163 TCGTGCGCAA
Statistics
Matches: 295, Mismatches: 37, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
309 291 0.99
310 4 0.01
ACGTcount: A:0.38, C:0.23, G:0.14, T:0.26
Consensus pattern (309 bp):
ATTTCAACTTCACAACGAAGGATACTGGACTCGAAACAATGCAACTTACACAAGATTGGATTTCA
AATTCACGACAAAGGATAACAAACTCAAAACCAATTTGGTGAAACAACCCTTGGATTTCAACTTC
ACAACGAAGGATATCCAATTCAAAGCTCAACTTCACAACAAAAGAGCCATCAACGATTTCAACTT
CACGAAGAAGGATATCATACCCACAAGCAGCATCCATCTCTAGATTGGATTTCAACTTCACAACG
AAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCATCCACG
Found at i:41378 original size:86 final size:86
Alignment explanation
Indices: 41266--41675 Score: 444
Period size: 86 Copynumber: 4.8 Consensus size: 86
41256 GTAAACCAAA
* *
41266 ACCTTCAAGTTCGATTACACTCAGCTCAAAGGCACATCAAATTTACAGCATAGCTCAAGATGAGA
1 ACCTTCGAGTTCGATTACATTCAGCTCAAAGGCACATCAAATTTACAGCATAGCTCAAGATGAGA
* * * *
41331 AGGGCTATCTATTAACAAACG
66 AGGGCTATCTGTCAAAAAAAG
* * * * *
41352 ACATTCGAGTTCGATTACATTCAGCTCTAAGGCACATCAAATTTACAGCATAACTTAAGGTGAGA
1 ACCTTCGAGTTCGATTACATTCAGCTCAAAGGCACATCAAATTTACAGCATAGCTCAAGATGAGA
** * *
41417 AGGATTATCTGTCCACAAAAG
66 AGGGCTATCTGTCAAAAAAAG
* * *
41438 ACCTTCGAGTTCGATTACATTCAGCTCAAATGCAAATCAAATTTACAGCATAGCTCAAGACGAGA
1 ACCTTCGAGTTCGATTACATTCAGCTCAAAGGCACATCAAATTTACAGCATAGCTCAAGATGAGA
* *
41503 ATGGCTATATGTCAAAAAAAG
66 AGGGCTATCTGTCAAAAAAAG
* * * * * **
41524 ACCTTCTAGTTCGATTACATTCAGCTTAAAGGCATATTC-GATTTATAGCATAGCTCAAGGCGAG
1 ACCTTCGAGTTCGATTACATTCAGCTCAAAGGCACA-TCAAATTTACAGCATAGCTCAAGATGAG
* *
41588 AAGGGATATCCGTCAAAAAAAG
65 AAGGGCTATCTGTCAAAAAAAG
* * * * * ** * * * *
41610 ACCTTCGAGTGCGATTACATACAACTCAAGGGAATGTCAAATTTACAACTTAGCTTAAGTTGAGA
1 ACCTTCGAGTTCGATTACATTCAGCTCAAAGGCACATCAAATTTACAGCATAGCTCAAGATGAGA
41675 A
66 A
41676 AATCTATATG
Statistics
Matches: 269, Mismatches: 53, Indels: 4
0.83 0.16 0.01
Matches are distributed among these distances:
85 2 0.01
86 265 0.99
87 2 0.01
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.26
Consensus pattern (86 bp):
ACCTTCGAGTTCGATTACATTCAGCTCAAAGGCACATCAAATTTACAGCATAGCTCAAGATGAGA
AGGGCTATCTGTCAAAAAAAG
Found at i:41591 original size:172 final size:172
Alignment explanation
Indices: 41229--41656 Score: 506
Period size: 172 Copynumber: 2.5 Consensus size: 172
41219 CCCAGTGCAT
* * * * * *
41229 CATAACTCAAGGCGAGAAGGGTTAACTGTAAACCAAA-ACCTTCAAGTTCGATTACACTCAGCTC
1 CATAACTCAAGGCGAGAAGGATTATCTGTCAACAAAAGACCTTCGAGTTCGATTACATTCAGCTC
* * * * * *
41293 AAAGGCACATCAAATTTACAGCATAGCTCAAGATGAGAAGGGCTATCTATTAACAAACGACATTC
66 AAAGGCAAATCAAATTTACAGCATAGCTCAAGACGAGAAGGGCTATATATCAAAAAAAGACATTC
41358 GAGTTCGATTACATTCAGCTCTAAGGCACATCAAATTTACAG
131 GAGTTCGATTACATTCAGCTCTAAGGCACATCAAATTTACAG
* * *
41400 CATAACTTAAGGTGAGAAGGATTATCTGTCCACAAAAGACCTTCGAGTTCGATTACATTCAGCTC
1 CATAACTCAAGGCGAGAAGGATTATCTGTCAACAAAAGACCTTCGAGTTCGATTACATTCAGCTC
* * * *
41465 AAATGCAAATCAAATTTACAGCATAGCTCAAGACGAGAATGGCTATATGTCAAAAAAAGACCTTC
66 AAAGGCAAATCAAATTTACAGCATAGCTCAAGACGAGAAGGGCTATATATCAAAAAAAGACATTC
* * * *
41530 TAGTTCGATTACATTCAGCT-TAAAGGCATATTC-GATTTATAG
131 GAGTTCGATTACATTCAGCTCT-AAGGCACA-TCAAATTTACAG
* * * * * *
41572 CATAGCTCAAGGCGAGAAGGGA-TATCCGTCAAAAAAAGACCTTCGAGTGCGATTACATACAACT
1 CATAACTCAAGGCGAGAA-GGATTATCTGTCAACAAAAGACCTTCGAGTTCGATTACATTCAGCT
* *
41636 C-AAGGGAATGTCAAATTTACA
65 CAAAGGCAA-ATCAAATTTACA
41657 ACTTAGCTTA
Statistics
Matches: 217, Mismatches: 35, Indels: 9
0.83 0.13 0.03
Matches are distributed among these distances:
171 36 0.17
172 176 0.81
173 5 0.02
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.25
Consensus pattern (172 bp):
CATAACTCAAGGCGAGAAGGATTATCTGTCAACAAAAGACCTTCGAGTTCGATTACATTCAGCTC
AAAGGCAAATCAAATTTACAGCATAGCTCAAGACGAGAAGGGCTATATATCAAAAAAAGACATTC
GAGTTCGATTACATTCAGCTCTAAGGCACATCAAATTTACAG
Found at i:43659 original size:17 final size:17
Alignment explanation
Indices: 43615--43660 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
43605 CCTTTACAGT
*
43615 TTTTAGTTATTTATTTA
1 TTTTATTTATTTATTTA
*
43632 TTTTATATATTTATTTA
1 TTTTATTTATTTATTTA
*
43649 TTTTTTTTATTT
1 TTTTATTTATTT
43661 TTAATATTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (17 bp):
TTTTATTTATTTATTTA
Found at i:47464 original size:20 final size:21
Alignment explanation
Indices: 47439--47484 Score: 85
Period size: 20 Copynumber: 2.2 Consensus size: 21
47429 ATTAAACTAT
47439 ATTATGGACTTGTAA-TTTTA
1 ATTATGGACTTGTAACTTTTA
47459 ATTATGGACTTGTAACTTTTA
1 ATTATGGACTTGTAACTTTTA
47480 ATTAT
1 ATTAT
47485 CGTGTATTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 15 0.60
21 10 0.40
ACGTcount: A:0.30, C:0.07, G:0.13, T:0.50
Consensus pattern (21 bp):
ATTATGGACTTGTAACTTTTA
Done.