Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003530.1 Hibiscus syriacus cultivar Beakdansim tig00007452_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: 121658
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:2190 original size:23 final size:24
Alignment explanation
Indices: 2164--2216 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
2154 TTAAACCTAG
* * *
2164 ACCGGTTTTTTTTCCTG-ATAAAA
1 ACCGGTTTTTTATCCGGTAAAAAA
2187 ACCGGTTTTTTATCCGGTAAAAAA
1 ACCGGTTTTTTATCCGGTAAAAAA
2211 ACCGGT
1 ACCGGT
2217 CTTGGTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 15 0.58
24 11 0.42
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (24 bp):
ACCGGTTTTTTATCCGGTAAAAAA
Found at i:2274 original size:20 final size:20
Alignment explanation
Indices: 2249--2288 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2239 GTTAAAATAA
* *
2249 CCGGTTTAAAAAAATCCGAT
1 CCGGTTAAAAAAAAACCGAT
2269 CCGGTTAAAAAAAAACCGAT
1 CCGGTTAAAAAAAAACCGAT
2289 TTTTCCTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.20, G:0.15, T:0.20
Consensus pattern (20 bp):
CCGGTTAAAAAAAAACCGAT
Found at i:11345 original size:21 final size:21
Alignment explanation
Indices: 11319--11360 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
11309 TGGGTCAGTG
11319 ACTTAAATGC-AAATTTTGAAA
1 ACTT-AATGCTAAATTTTGAAA
*
11340 ACTTAATGCTCAATTTTGAAA
1 ACTTAATGCTAAATTTTGAAA
11361 TAAGTTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.36
Consensus pattern (21 bp):
ACTTAATGCTAAATTTTGAAA
Found at i:13195 original size:18 final size:18
Alignment explanation
Indices: 13172--13240 Score: 102
Period size: 18 Copynumber: 3.8 Consensus size: 18
13162 AGGGATTTAC
13172 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
13190 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* * *
13208 AATGGTCCTTCGGGGCAA
1 AGTGGTCCTTCGGGACAT
*
13226 AGTGGTCATTCGGGA
1 AGTGGTCCTTCGGGA
13241 TAAACATTCA
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 45 1.00
ACGTcount: A:0.19, C:0.20, G:0.35, T:0.26
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:18340 original size:18 final size:17
Alignment explanation
Indices: 18317--18370 Score: 72
Period size: 18 Copynumber: 3.1 Consensus size: 17
18307 AGGGATTTAC
18317 AGTGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
*
18334 TAGTGGTCCTTCGGGATA
1 -AGTGGTCCTTCGGGACA
*
18352 ATGTGGTCTTTCGGGACA
1 A-GTGGTCCTTCGGGACA
18370 A
1 A
18371 ACATTTAGTG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
17 1 0.03
18 31 0.97
ACGTcount: A:0.19, C:0.19, G:0.33, T:0.30
Consensus pattern (17 bp):
AGTGGTCCTTCGGGACA
Found at i:36635 original size:18 final size:19
Alignment explanation
Indices: 36600--36636 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
36590 CACGGAATGT
36600 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
36620 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
36637 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:36809 original size:15 final size:16
Alignment explanation
Indices: 36791--36826 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
36781 AAATTCTAAA
36791 TATTTAAATAAAATT-
1 TATTTAAATAAAATTC
*
36806 TATTTATATAAAATTC
1 TATTTAAATAAAATTC
36822 TATTT
1 TATTT
36827 TTTGATAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 14 0.74
16 5 0.26
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (16 bp):
TATTTAAATAAAATTC
Found at i:46393 original size:42 final size:40
Alignment explanation
Indices: 46341--46518 Score: 171
Period size: 42 Copynumber: 4.3 Consensus size: 40
46331 GATTTACATA
* * * *
46341 TTCGCATTGCGATAGTCCAAGTTCGCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATATTCCAAATT--CGTTGCGATAGTCCAAG
* *
46383 TTCGCGTTGCGATTTTTCAAATTCGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATATTCCAAATTCGTTGCGATAGTCCAAG
*** * *
46423 TTCGCGTTATAATTTATTCTAAATTTGTTGCGATAGTCCAAG
1 TTCGCGTTGCGA--TATTCCAAATTCGTTGCGATAGTCCAAG
* *
46465 TTCGCGTTGCGATTTATTACAAATTCGTTGCGATAGTCTAAG
1 TTCGCGTTGCGA--TATTCCAAATTCGTTGCGATAGTCCAAG
46507 TT--CGTTGCGATA
1 TTCGCGTTGCGATA
46519 GTCGAAGTTC
Statistics
Matches: 114, Mismatches: 20, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
38 2 0.02
40 33 0.29
42 79 0.69
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.37
Consensus pattern (40 bp):
TTCGCGTTGCGATATTCCAAATTCGTTGCGATAGTCCAAG
Found at i:46417 original size:40 final size:41
Alignment explanation
Indices: 46366--46517 Score: 211
Period size: 42 Copynumber: 3.7 Consensus size: 41
46356 TCCAAGTTCG
*
46366 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTT-TTCAAATT
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCAAATT
***
46406 CGTTGCGATAGTCCAAGTTCGCGTTATAATTTATTCTAAATT
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTC-AAATT
*
46448 TGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTACAAATT
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATT-CAAATT
*
46490 CGTTGCGATAGTCTAAGTT--CGTTGCGAT
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGAT
46518 AGTCGAAGTT
Statistics
Matches: 99, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
40 37 0.37
41 3 0.03
42 58 0.59
43 1 0.01
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.38
Consensus pattern (41 bp):
CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCAAATT
Found at i:46505 original size:61 final size:61
Alignment explanation
Indices: 46440--46572 Score: 194
Period size: 61 Copynumber: 2.2 Consensus size: 61
46430 TATAATTTAT
* * *
46440 TCTAAATTTGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTACAAATTCGTTGCGATAG
1 TCTAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTCATTACAAATTCGTTACGATAG
* * *
46501 TCTAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTCATTCCAAATTCGTTACGATAG
1 TCTAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTCATTACAAATTCGTTACGATAG
* *
46562 TCCAAAATCGT
1 TCTAAATTCGT
46573 AACGACTGGT
Statistics
Matches: 63, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
61 63 1.00
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (61 bp):
TCTAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTCATTACAAATTCGTTACGATAG
Found at i:46527 original size:103 final size:102
Alignment explanation
Indices: 46347--46566 Score: 257
Period size: 103 Copynumber: 2.1 Consensus size: 102
46337 CATATTCGCA
* * *
46347 TTGCGATAGTCCAAGTTCGCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTTCAAATTCGTTGC
1 TTGCGATAGTCCAAGTTCGCGTTGCGATAGTCGAAATTC-CGTTGCGATGTCTCAAATTCGTTGC
* * * *
46412 GATAGTCCAAGTTCGCGTTATAATTTATTCTAAATTTG
65 GATAGTCCAAGTTCGCGTTACAATTCATTCCAAATTCG
* *
46450 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTAC-AAATT-CGTTGCGATAGTCT-AAGTTCGT
1 TTGCGATAGTCCAAGTTCGCGTTGCGA--TAGT-CGAAATTCCGTTGCGAT-GTCTCAAATTCGT
* * *
46512 TGCGATAGTCGAAGTTCGCGTTGCGATTCATTCCAAATTCG
62 TGCGATAGTCCAAGTTCGCGTTACAATTCATTCCAAATTCG
*
46553 TTACGATAGTCCAA
1 TTGCGATAGTCCAA
46567 AATCGTAACG
Statistics
Matches: 100, Mismatches: 13, Indels: 8
0.83 0.11 0.07
Matches are distributed among these distances:
103 90 0.90
104 2 0.02
105 7 0.07
106 1 0.01
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.36
Consensus pattern (102 bp):
TTGCGATAGTCCAAGTTCGCGTTGCGATAGTCGAAATTCCGTTGCGATGTCTCAAATTCGTTGCG
ATAGTCCAAGTTCGCGTTACAATTCATTCCAAATTCG
Found at i:46567 original size:19 final size:19
Alignment explanation
Indices: 46347--46572 Score: 101
Period size: 21 Copynumber: 11.1 Consensus size: 19
46337 CATATTCGCA
*
46347 TTGCGATAGTCCAAGTTCGCG
1 TTGCGATAGTCCAAATT--CG
* *
46368 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAATT--CG
** *
46389 TTGCGATTTTTCAAATTCG
1 TTGCGATAGTCCAAATTCG
*
46408 TTGCGATAGTCCAAGTTCGCG
1 TTGCGATAGTCCAAATT--CG
*** * * *
46429 TTATAATTTATTCTAAATTTG
1 TTGCGA--TAGTCCAAATTCG
*
46450 TTGCGATAGTCCAAGTTCGCG
1 TTGCGATAGTCCAAATT--CG
* *
46471 TTGCGATTTATTACAAATTCG
1 TTGCGA--TAGTCCAAATTCG
* *
46492 TTGCGATAGTCTAAGTTCG
1 TTGCGATAGTCCAAATTCG
* *
46511 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAATT--CG
*
46532 TTGCGATTCATTCCAAATTCG
1 TTGCGA-T-AGTCCAAATTCG
* *
46553 TTACGATAGTCCAAAATCG
1 TTGCGATAGTCCAAATTCG
46572 T
1 T
46573 AACGACTGGT
Statistics
Matches: 155, Mismatches: 38, Indels: 26
0.71 0.17 0.12
Matches are distributed among these distances:
19 59 0.38
20 1 0.01
21 71 0.46
22 1 0.01
23 23 0.15
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.36
Consensus pattern (19 bp):
TTGCGATAGTCCAAATTCG
Found at i:49242 original size:18 final size:18
Alignment explanation
Indices: 49219--49259 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
49209 ACCTATTTCT
49219 GGTGAAGATGATGTATCC
1 GGTGAAGATGATGTATCC
49237 GGTGAAGATGATGTATCC
1 GGTGAAGATGATGTATCC
49255 GGTGA
1 GGTGA
49260 TGGGTCTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.10, G:0.37, T:0.27
Consensus pattern (18 bp):
GGTGAAGATGATGTATCC
Found at i:53252 original size:8 final size:8
Alignment explanation
Indices: 53239--53266 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
53229 TTATTATTAT
53239 TATTTTAA
1 TATTTTAA
53247 TATTTTAA
1 TATTTTAA
53255 TATTTTAA
1 TATTTTAA
53263 TATT
1 TATT
53267 ATTATTTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (8 bp):
TATTTTAA
Found at i:55281 original size:30 final size:31
Alignment explanation
Indices: 55239--55302 Score: 96
Period size: 30 Copynumber: 2.1 Consensus size: 31
55229 GTCTTTATTA
55239 TTATTCTTCTCCCCTGTATATACATATA-AT
1 TTATTCTTCTCCCCTGTATATACATATATAT
*
55269 TTATT-TTCCTCCCCTGTATATACATTTATAT
1 TTATTCTT-CTCCCCTGTATATACATATATAT
55300 TTA
1 TTA
55303 AATATATATT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
29 2 0.06
30 24 0.77
31 5 0.16
ACGTcount: A:0.25, C:0.22, G:0.03, T:0.50
Consensus pattern (31 bp):
TTATTCTTCTCCCCTGTATATACATATATAT
Found at i:60161 original size:15 final size:15
Alignment explanation
Indices: 60141--60170 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
60131 TATTTCTTTG
*
60141 TTATTTTATTTAATT
1 TTATTTTATTCAATT
60156 TTATTTTATTCAATT
1 TTATTTTATTCAATT
60171 AAATTCGATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (15 bp):
TTATTTTATTCAATT
Found at i:60329 original size:21 final size:22
Alignment explanation
Indices: 60290--60330 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
60280 ATTATTTTTA
*
60290 TTTATTTAAATTGAGAATTATG
1 TTTATTTAAATTGACAATTATG
*
60312 TTTATTT-ATTTGACAATTA
1 TTTATTTAAATTGACAATTA
60331 CGATGTTTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.34, C:0.02, G:0.10, T:0.54
Consensus pattern (22 bp):
TTTATTTAAATTGACAATTATG
Found at i:60584 original size:140 final size:140
Alignment explanation
Indices: 60431--60691 Score: 334
Period size: 142 Copynumber: 1.9 Consensus size: 140
60421 TAAACATAGG
* *
60431 ATAAATGAAAAATATGTATTTAACTTGAC-AGATACGGA-A-AATAATATGAGATGATATGATAA
1 ATAAATGAAAAATATGTATTT-ACTTGACGAGATA-AGATATAATAATACGAGATGATATGATAA
** *
60493 ATTCAAA-TGAGAATTAAATGTATAGTTTCTTTTTCTTTAATCTT-CTATTCATTTTCCTAATAC
64 ATT-AAACCAAGAATTAAATGTATAGTTTC-TTTTATTTAA-CTTCCTATTCATTTTCCTAATAC
60556 TTGTATAAACGAAGA
126 TTGTATAAACGAAGA
* * * *
60571 ATAAATGAAAAATATGTATTTAGTTTACTGAGATAAGATATAATAATACGAGGTGATATTATAAA
1 ATAAATGAAAAATATGTATTTACTTGAC-GAGATAAGATATAATAATACGAGATGATATGATAAA
* *
60636 TTAAACCAAGAATTAAATGTATCGTTTCTTTTATTTAACTTCCTGTTCATTTTCCT
65 TTAAACCAAGAATTAAATGTATAGTTTCTTTTATTTAACTTCCTATTCATTTTCCT
60692 TTATTAATAC
Statistics
Matches: 104, Mismatches: 11, Indels: 11
0.83 0.09 0.09
Matches are distributed among these distances:
139 5 0.05
140 26 0.25
141 31 0.30
142 42 0.40
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (140 bp):
ATAAATGAAAAATATGTATTTACTTGACGAGATAAGATATAATAATACGAGATGATATGATAAAT
TAAACCAAGAATTAAATGTATAGTTTCTTTTATTTAACTTCCTATTCATTTTCCTAATACTTGTA
TAAACGAAGA
Found at i:68500 original size:16 final size:16
Alignment explanation
Indices: 68479--68516 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
68469 TTTTGTTGCC
68479 ATAGCTTCTTTTACGG
1 ATAGCTTCTTTTACGG
68495 ATAGCTTCTTTTACGG
1 ATAGCTTCTTTTACGG
68511 ATAGCT
1 ATAGCT
68517 CCCACTATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.21, C:0.18, G:0.18, T:0.42
Consensus pattern (16 bp):
ATAGCTTCTTTTACGG
Found at i:73903 original size:20 final size:20
Alignment explanation
Indices: 73867--73904 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
73857 ATGCTATTCC
**
73867 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
73887 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
73905 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:89660 original size:9 final size:9
Alignment explanation
Indices: 89643--89681 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
89633 AGATAGCATC
*
89643 AAAATTAAT
1 AAAAATAAT
89652 AAAAATAAT
1 AAAAATAAT
*
89661 AATAATAAT
1 AAAAATAAT
*
89670 AATAATAAT
1 AAAAATAAT
89679 AAA
1 AAA
89682 TACGTATTGC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (9 bp):
AAAAATAAT
Found at i:89663 original size:3 final size:3
Alignment explanation
Indices: 89648--89680 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
89638 GCATCAAAAT
*
89648 TAA TAA AAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
89681 ATACGTATTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:95074 original size:55 final size:54
Alignment explanation
Indices: 95005--95285 Score: 282
Period size: 55 Copynumber: 5.1 Consensus size: 54
94995 AGGATAAGCG
* * * *
95005 AGACTTGAAAAATCTTCAA-ATAACGGGTCTGTTCCCTATTCTTTTAAGGAGTATA
1 AGACTCGAACAATCTTCAACA-AACGGGTCTGCTCCCTATTC-TTCAAGGAGTATA
*** * *
95060 AGACTCGAACAATCTTTGGCAAACGTGTCTGCTCCCTATTCATTCAGGGAGTATA
1 AGACTCGAACAATCTTCAACAAACGGGTCTGCTCCCTATTC-TTCAAGGAGTATA
* * *
95115 AGACTCAAACAATCTTCAACAAACGTGTCTGCTCCCTATTCGTTCAGGGAGTATA
1 AGACTCGAACAATCTTCAACAAACGGGTCTGCTCCCTATTC-TTCAAGGAGTATA
* * *
95170 AGACTCGAATAATCTTCAACAAACGGGTCCGCTCTCTATTCCTTC-AGAGAGTAT-
1 AGACTCGAACAATCTTCAACAAACGGGTCTGCTCCCTATT-CTTCAAG-GAGTATA
** *
95224 AGAACTCGAACAATCTTCAACAAACTTGTCCGCTCCCTATTCCTTC-AGAGAGTATA
1 AG-ACTCGAACAATCTTCAACAAACGGGTCTGCTCCCTATT-CTTCAAG-GAGTATA
*
95280 GGACTC
1 AGACTC
95286 AATCTTTAAC
Statistics
Matches: 195, Mismatches: 26, Indels: 10
0.84 0.11 0.04
Matches are distributed among these distances:
54 3 0.02
55 189 0.97
56 3 0.02
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (54 bp):
AGACTCGAACAATCTTCAACAAACGGGTCTGCTCCCTATTCTTCAAGGAGTATA
Found at i:95185 original size:110 final size:108
Alignment explanation
Indices: 95015--95387 Score: 386
Period size: 110 Copynumber: 3.5 Consensus size: 108
95005 AGACTTGAAA
* * * * *
95015 AATCTTCAA-ATAACGGGTCTGTTCCCTATTCTTTTA-AGGAGTATAAGACTCGAACAATCTTTG
1 AATCTTCAACA-AACGTGTCTGCTCCCTATTCCTTCAGA-GAGTATAAGACTCGAA-AATCTTTA
* * * *
95078 GCAAACGTGTCTGCTCCCTATTCATTCAGGGAGTATAAGACTCAAAC
63 ACAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTC-AAC
* * *
95125 AATCTTCAACAAACGTGTCTGCTCCCTATTCGTTCAGGGAGTATAAGACTCGAATAATCTTCAAC
1 AATCTTCAACAAACGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAA-AATCTTTAAC
* *
95190 AAACGGGTCCGCTCTCTATTCCTTCAGAGAGTAT-AGAACTCGAAC
65 AAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAAG-ACTC-AAC
* * * *
95235 AATCTTCAACAAACTTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTC---AATCTTTAACG
1 AATCTTCAACAAACGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAAAATCTTTAACA
* * * *
95297 AACTTGTCCACTCCATATTCCTTCAGAGAGTATAGGACT---C
66 AACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCAAC
* * * *
95337 AATCTTCAACGAACTTGTCTGTTCCCTATTCCTTCAGAGAGTATAGGACTC
1 AATCTTCAACAAACGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTC
95388 AATCTTCAAC
Statistics
Matches: 228, Mismatches: 31, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
102 49 0.21
106 40 0.18
107 1 0.00
109 2 0.01
110 135 0.59
111 1 0.00
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (108 bp):
AATCTTCAACAAACGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAAAATCTTTAACA
AACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCAAC
Found at i:95316 original size:51 final size:51
Alignment explanation
Indices: 95085--95397 Score: 329
Period size: 55 Copynumber: 5.9 Consensus size: 51
95075 TTGGCAAACG
* * * * * *
95085 TGTCTGCTCCCTATTCATTCAGGGAGTATAAGACTCAAACAATCTTCAACAAACG
1 TGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACT----CAATCTTCAACGAACT
* * * * * *
95140 TGTCTGCTCCCTATTCGTTCAGGGAGTATAAGACTCGAATAATCTTCAACAAACG
1 TGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTC----AATCTTCAACGAACT
* * * *
95195 GGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACT
1 TGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACT----CAATCTTCAACGAACT
*
95250 TGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTTAACGAACT
1 TGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACT
* *
95301 TGTCCACTCCATATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACT
1 TGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACT
* *
95352 TGTCTGTTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAAC
1 TGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAAC
95398 AAATGAATTT
Statistics
Matches: 229, Mismatches: 21, Indels: 20
0.85 0.08 0.07
Matches are distributed among these distances:
51 105 0.46
55 123 0.54
59 1 0.00
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.30
Consensus pattern (51 bp):
TGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACT
Found at i:95365 original size:102 final size:103
Alignment explanation
Indices: 95123--95400 Score: 353
Period size: 102 Copynumber: 2.6 Consensus size: 103
95113 TAAGACTCAA
* * * *
95123 ACAATCTTCAACAAACGTGTCTGCTCCCTATTCGTTCAGGGAGTATAAGACTCGAATAATCTTCA
1 ACAATCTTCAACAAACTTGTCTGCTCCCTATTCCTTCAGAGAGTATAGGACTC----AATCTTCA
*
95188 ACAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACT
62 ACAAACGGGTCCACTCTCTATTCCTTCAGAGAGTATAGAACT
* *
95230 CGAACAATCTTCAACAAACTTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTTAA
1 ---ACAATCTTCAACAAACTTGTCTGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAA
* ** *
95295 CGAACTTGTCCACTC-CATATTCCTTCAGAGAGTATAGGACT
63 CAAACGGGTCCACTCTC-TATTCCTTCAGAGAGTATAGAACT
* *
95336 -CAATCTTCAACGAACTTGTCTGTTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACAA
1 ACAATCTTCAACAAACTTGTCTGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACAA
95400 A
66 A
95401 TGAATTTGCT
Statistics
Matches: 151, Mismatches: 16, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
102 60 0.40
105 1 0.01
106 42 0.28
110 48 0.32
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.29
Consensus pattern (103 bp):
ACAATCTTCAACAAACTTGTCTGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACAA
ACGGGTCCACTCTCTATTCCTTCAGAGAGTATAGAACT
Found at i:96739 original size:7 final size:7
Alignment explanation
Indices: 96727--96759 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
96717 TATTTCTCTT
96727 TTTTTCA
1 TTTTTCA
*
96734 TTTTTCT
1 TTTTTCA
96741 TTTTTCA
1 TTTTTCA
96748 TTTTTCA
1 TTTTTCA
96755 TTTTT
1 TTTTT
96760 TTCTTCCCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.09, C:0.12, G:0.00, T:0.79
Consensus pattern (7 bp):
TTTTTCA
Found at i:96743 original size:14 final size:15
Alignment explanation
Indices: 96726--96760 Score: 63
Period size: 14 Copynumber: 2.4 Consensus size: 15
96716 TTATTTCTCT
96726 TTTTTTCATTTTTC-
1 TTTTTTCATTTTTCA
96740 TTTTTTCATTTTTCA
1 TTTTTTCATTTTTCA
96755 TTTTTT
1 TTTTTT
96761 TCTTCCCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 14 0.70
15 6 0.30
ACGTcount: A:0.09, C:0.11, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTTTTCATTTTTCA
Found at i:96771 original size:20 final size:20
Alignment explanation
Indices: 96727--96784 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
96717 TATTTCTCTT
* *
96727 TTTTTCATTTTTCTTTTTTCA
1 TTTTTCATTTTT-TTCTTCCA
*
96748 TTTTTCATTTTTTTCTTCCC
1 TTTTTCATTTTTTTCTTCCA
*
96768 TTTTCCATTTTTTTCTT
1 TTTTTCATTTTTTTCTT
96785 TTCGTTTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
20 21 0.64
21 12 0.36
ACGTcount: A:0.07, C:0.19, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTTTCATTTTTTTCTTCCA
Found at i:96810 original size:18 final size:17
Alignment explanation
Indices: 96725--96821 Score: 57
Period size: 14 Copynumber: 5.9 Consensus size: 17
96715 TTTATTTCTC
96725 TTTTTT-TCATTTTTC-
1 TTTTTTCTCATTTTTCG
*
96740 -TTTTT-TCATTTTTCAT
1 TTTTTTCTCATTTTTC-G
* * *
96756 TTTTTTCTTCCCTTTTCCA
1 TTTTTTC-T-CATTTTTCG
96775 TTTTTT-TC--TTTTCG
1 TTTTTTCTCATTTTTCG
96789 TTTTTTCCATCATTTTTC-
1 TTTTTT-C-TCATTTTTCG
96807 TTTTTTCTCATTTTT
1 TTTTTTCTCATTTTT
96822 TCTCTTTTAT
Statistics
Matches: 66, Mismatches: 5, Indels: 21
0.72 0.05 0.23
Matches are distributed among these distances:
14 24 0.36
16 9 0.14
17 9 0.14
18 6 0.09
19 12 0.18
20 6 0.09
ACGTcount: A:0.07, C:0.19, G:0.01, T:0.73
Consensus pattern (17 bp):
TTTTTTCTCATTTTTCG
Found at i:96822 original size:17 final size:17
Alignment explanation
Indices: 96783--96829 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 17
96773 CATTTTTTTC
96783 TTTTCGTTTTTTCCATCAT
1 TTTTC-TTTTTTCCAT-AT
96802 TTTTCTTTTTTCTCAT-T
1 TTTTCTTTTTTC-CATAT
96819 TTTTCTCTTTT
1 TTTTCT-TTTT
96830 ATTTCTTCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 7 0.27
18 11 0.42
19 8 0.31
ACGTcount: A:0.06, C:0.19, G:0.02, T:0.72
Consensus pattern (17 bp):
TTTTCTTTTTTCCATAT
Found at i:96822 original size:18 final size:18
Alignment explanation
Indices: 96783--96821 Score: 55
Period size: 16 Copynumber: 2.2 Consensus size: 18
96773 CATTTTTTTC
96783 TTTTCGTTTTTTCCATCAT
1 TTTTC-TTTTTTCCATCAT
96802 TTTTCTTTTTT-C-TCAT
1 TTTTCTTTTTTCCATCAT
96818 TTTT
1 TTTT
96822 TCTCTTTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 8 0.40
17 1 0.05
18 6 0.30
19 5 0.25
ACGTcount: A:0.08, C:0.18, G:0.03, T:0.72
Consensus pattern (18 bp):
TTTTCTTTTTTCCATCAT
Found at i:96822 original size:43 final size:40
Alignment explanation
Indices: 96717--96833 Score: 100
Period size: 41 Copynumber: 2.9 Consensus size: 40
96707 ACCCTCCTTT
* *
96717 TATTTCTCTTTTTT-TCATTTTTCTT-TTTTCATTTTTCA
1 TATTTTTCTTTTTTCTCATTTTTTTTCTTTTCATTTTTCA
* *
96755 TTTTTTTCTTCCCTTTTC-CA-TTTTTTTCTTTTCGTTTTTTCCA
1 TATTTTTCTT---TTTTCTCATTTTTTTTCTTTTC-ATTTTT-CA
*
96798 TCATTTTTCTTTTTTCTCATTTTTTCTCTTTT-ATTT
1 T-ATTTTTCTTTTTTCTCATTTTTTTTCTTTTCATTT
96834 CTTCTTCAAG
Statistics
Matches: 62, Mismatches: 7, Indels: 17
0.72 0.08 0.20
Matches are distributed among these distances:
38 8 0.13
40 6 0.10
41 19 0.31
42 7 0.11
43 14 0.23
44 8 0.13
ACGTcount: A:0.08, C:0.19, G:0.01, T:0.73
Consensus pattern (40 bp):
TATTTTTCTTTTTTCTCATTTTTTTTCTTTTCATTTTTCA
Found at i:111723 original size:35 final size:35
Alignment explanation
Indices: 111671--111778 Score: 125
Period size: 35 Copynumber: 3.2 Consensus size: 35
111661 CAAAACAGTC
*
111671 TTCAATTTCATTGTAAACCCCAATTTCCAAAGTAA
1 TTCAATTTCATTCTAAACCCCAATTTCCAAAGTAA
* *
111706 TTCACTTTCATTCTAAACCCTAATTTCCAAAGTAA
1 TTCAATTTCATTCTAAACCCCAATTTCCAAAGTAA
* * * *
111741 TTTAA--T--TTCTAAACCCTAAATTCCAAAATAA
1 TTCAATTTCATTCTAAACCCCAATTTCCAAAGTAA
111772 TTCAATT
1 TTCAATT
111779 AAATTTTAAA
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
31 27 0.43
33 1 0.02
35 35 0.56
ACGTcount: A:0.38, C:0.22, G:0.03, T:0.37
Consensus pattern (35 bp):
TTCAATTTCATTCTAAACCCCAATTTCCAAAGTAA
Found at i:111754 original size:31 final size:31
Alignment explanation
Indices: 111684--111778 Score: 109
Period size: 31 Copynumber: 2.9 Consensus size: 31
111674 AATTTCATTG
* *
111684 TAAACCCCAATTTCCAAAGTAATTCACTTTCATTC
1 TAAACCCTAATTTCCAAAGTAATTCA--AT--TTC
*
111719 TAAACCCTAATTTCCAAAGTAATTTAATTTC
1 TAAACCCTAATTTCCAAAGTAATTCAATTTC
* *
111750 TAAACCCTAAATTCCAAAATAATTCAATT
1 TAAACCCTAATTTCCAAAGTAATTCAATT
111779 AAATTTTAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
31 29 0.54
33 1 0.02
35 24 0.44
ACGTcount: A:0.40, C:0.23, G:0.02, T:0.35
Consensus pattern (31 bp):
TAAACCCTAATTTCCAAAGTAATTCAATTTC
Found at i:111797 original size:35 final size:36
Alignment explanation
Indices: 111739--111813 Score: 91
Period size: 35 Copynumber: 2.1 Consensus size: 36
111729 TTTCCAAAGT
* *
111739 AATTTAATTTCTAAACCCTAAATTCCAAAATAATTC
1 AATTAAATTTCTAAACCCTAAATTCCAAAACAATTC
* *
111775 AATTAAATTT-TAAACTCC-AAATTCTAAAACACTTC
1 AATTAAATTTCTAAAC-CCTAAATTCCAAAACAATTC
111810 AATT
1 AATT
111814 TAAGGTTTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
35 23 0.68
36 11 0.32
ACGTcount: A:0.45, C:0.19, G:0.00, T:0.36
Consensus pattern (36 bp):
AATTAAATTTCTAAACCCTAAATTCCAAAACAATTC
Done.