Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001934.1 Hibiscus syriacus cultivar Beakdansim tig00003918_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: 89548
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1133 original size:43 final size:43
Alignment explanation
Indices: 1041--1160 Score: 152
Period size: 43 Copynumber: 2.8 Consensus size: 43
1031 TGAAGTATTT
* * *
1041 ATGTTATCTACATGGGATCCTCTATGGATGGT-ATATCCCTATC
1 ATGTT-TCTACATGGGATCCTCTACGGAGGGTAATATCCCCATC
* **
1084 CTGTTTCTGTATGGGATCCTCTACGGAGGGTAATATCCCCATC
1 ATGTTTCTACATGGGATCCTCTACGGAGGGTAATATCCCCATC
* *
1127 ATGTTTCTACATAGGATGCTCTACGGAGGGTAAT
1 ATGTTTCTACATGGGATCCTCTACGGAGGGTAAT
1161 GTATTTGTCC
Statistics
Matches: 65, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
42 22 0.34
43 43 0.66
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.34
Consensus pattern (43 bp):
ATGTTTCTACATGGGATCCTCTACGGAGGGTAATATCCCCATC
Found at i:3964 original size:24 final size:24
Alignment explanation
Indices: 3918--3965 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
3908 GTAGTTGATC
*
3918 AAATTATTCTAGATTAAAATAAAT
1 AAATTATTCTAGATCAAAATAAAT
* * *
3942 AAATTATTTTGGATCAAAGTAAAT
1 AAATTATTCTAGATCAAAATAAAT
3966 GGATTAGTCA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.50, C:0.04, G:0.08, T:0.38
Consensus pattern (24 bp):
AAATTATTCTAGATCAAAATAAAT
Found at i:5322 original size:20 final size:20
Alignment explanation
Indices: 5299--5345 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
5289 TAAATCCATG
*
5299 AAATCATCTTA-AAACTTCCA
1 AAATCAT-TTATAAACTTACA
* *
5319 AAATTATTTATAATCTTACA
1 AAATCATTTATAAACTTACA
5339 AAATCAT
1 AAATCAT
5346 AGAATGGGTT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 3 0.14
20 19 0.86
ACGTcount: A:0.47, C:0.17, G:0.00, T:0.36
Consensus pattern (20 bp):
AAATCATTTATAAACTTACA
Found at i:11966 original size:15 final size:14
Alignment explanation
Indices: 11946--12000 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 14
11936 AATTATTTTA
11946 TTTTATTTTTTACTT
1 TTTTATTTTTTA-TT
11961 TTTTATTTTTATAGTAT
1 TTTTATTTTT-TA-T-T
* *
11978 TTTGATTTTTTATA
1 TTTTATTTTTTATT
11992 TTTTATTTT
1 TTTTATTTT
12001 AAATTAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
14 8 0.24
15 11 0.32
16 5 0.15
17 10 0.29
ACGTcount: A:0.18, C:0.02, G:0.04, T:0.76
Consensus pattern (14 bp):
TTTTATTTTTTATT
Found at i:11969 original size:7 final size:7
Alignment explanation
Indices: 11946--12000 Score: 56
Period size: 7 Copynumber: 7.3 Consensus size: 7
11936 AATTATTTTA
11946 TTTTATT
1 TTTTATT
11953 TTTTACTT
1 TTTTA-TT
11961 TTTTATT
1 TTTTATT
11968 TTTATAGTAT
1 TTT-TA-T-T
*
11978 TTTGATT
1 TTTTATT
*
11985 TTTTATA
1 TTTTATT
11992 TTTTATT
1 TTTTATT
11999 TT
1 TT
12001 AAATTAAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
7 24 0.60
8 10 0.25
9 2 0.05
10 4 0.10
ACGTcount: A:0.18, C:0.02, G:0.04, T:0.76
Consensus pattern (7 bp):
TTTTATT
Found at i:19311 original size:23 final size:23
Alignment explanation
Indices: 19249--19299 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
19239 CAATATGAAT
19249 GAGAAGAAACTAGAAAATAAATA
1 GAGAAGAAACTAGAAAATAAATA
19272 GAGAAGAAACTAGAAAATAAATA
1 GAGAAGAAACTAGAAAATAAATA
19295 GAGAA
1 GAGAA
19300 AATTTTGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.65, C:0.04, G:0.20, T:0.12
Consensus pattern (23 bp):
GAGAAGAAACTAGAAAATAAATA
Found at i:22998 original size:20 final size:20
Alignment explanation
Indices: 22973--23018 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
22963 ATTATGGTTT
22973 AATTATTTGAAAAAATATAA
1 AATTATTTGAAAAAATATAA
22993 AATTATTTGAAAAAATATAA
1 AATTATTTGAAAAAATATAA
23013 AATTAT
1 AATTAT
23019 AAACCAACAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (20 bp):
AATTATTTGAAAAAATATAA
Found at i:32329 original size:30 final size:30
Alignment explanation
Indices: 32282--32371 Score: 137
Period size: 30 Copynumber: 3.0 Consensus size: 30
32272 AAATTTTAAA
32282 TAAATTCAATT-AAGTCCAAATACATTTTG
1 TAAATTCAATTCAAGTCCAAATACATTTTG
* *
32311 TAAATTTAATTCAAGTCCAAATACGTTTTG
1 TAAATTCAATTCAAGTCCAAATACATTTTG
*
32341 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAATA-CATTTTG
32372 CCTTAAATTG
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
29 10 0.19
30 38 0.70
31 6 0.11
ACGTcount: A:0.40, C:0.16, G:0.08, T:0.37
Consensus pattern (30 bp):
TAAATTCAATTCAAGTCCAAATACATTTTG
Found at i:34704 original size:30 final size:30
Alignment explanation
Indices: 34657--34746 Score: 137
Period size: 30 Copynumber: 3.0 Consensus size: 30
34647 AAATTTTGAA
34657 TAAATTCAATT-AAGTCCAAATACATTTTG
1 TAAATTCAATTCAAGTCCAAATACATTTTG
* *
34686 TAAATTTAATTCAAGTCCAAATACGTTTTG
1 TAAATTCAATTCAAGTCCAAATACATTTTG
*
34716 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAATA-CATTTTG
34747 CCTTAAATTG
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
29 10 0.19
30 38 0.70
31 6 0.11
ACGTcount: A:0.40, C:0.16, G:0.08, T:0.37
Consensus pattern (30 bp):
TAAATTCAATTCAAGTCCAAATACATTTTG
Found at i:38295 original size:21 final size:21
Alignment explanation
Indices: 38246--38296 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
38236 TCATAATTTG
38246 AATA-ATA-AAACAACAACAA
1 AATATATATAAACAACAACAA
* *
38265 GATCTATATAAACAACAACAA
1 AATATATATAAACAACAACAA
38286 CAATAT-TATAA
1 -AATATATATAA
38297 TTCAAATCAA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 2 0.08
20 3 0.12
21 17 0.68
22 3 0.12
ACGTcount: A:0.63, C:0.16, G:0.02, T:0.20
Consensus pattern (21 bp):
AATATATATAAACAACAACAA
Found at i:40271 original size:16 final size:16
Alignment explanation
Indices: 40250--40282 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
40240 CGCTAAAATA
40250 ATATTTTATTCATTAT
1 ATATTTTATTCATTAT
*
40266 ATATTTTATTGATTAT
1 ATATTTTATTCATTAT
40282 A
1 A
40283 CCTACCATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.61
Consensus pattern (16 bp):
ATATTTTATTCATTAT
Found at i:44397 original size:33 final size:33
Alignment explanation
Indices: 44359--44475 Score: 155
Period size: 33 Copynumber: 3.5 Consensus size: 33
44349 AGTTGAAAAA
44359 TTCATCTTGGTTGGTGGGCAACTTATTGGAAAT
1 TTCATCTTGGTTGGTGGGCAACTTATTGGAAAT
* *
44392 TTCATCTTTGTTGGT-AGCTAACTTATTGGAAAT
1 TTCATCTTGGTTGGTGGGC-AACTTATTGGAAAT
* **
44425 TTCATCTTAGTTGGTGTCCAACTTATTGGAAAT
1 TTCATCTTGGTTGGTGGGCAACTTATTGGAAAT
*
44458 TTCATCTTTGGTAGGTGG
1 TTCATC-TTGGTTGGTGG
44476 CTAACTTTGC
Statistics
Matches: 73, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
32 2 0.03
33 62 0.85
34 9 0.12
ACGTcount: A:0.21, C:0.13, G:0.23, T:0.43
Consensus pattern (33 bp):
TTCATCTTGGTTGGTGGGCAACTTATTGGAAAT
Found at i:47180 original size:65 final size:64
Alignment explanation
Indices: 47089--47241 Score: 177
Period size: 64 Copynumber: 2.4 Consensus size: 64
47079 TACATTAGGG
* * * * *
47089 GTGCATCGGTGCACTAATTACATTCGATGTTTC-AAATGA-GCATGGAGTGCATAAATGCATGG-
1 GTGCATCGGTGCACAAAATGCATTCGAT-ATTCAAAAT-ATGCA-AGAGTGCATAAATGCATGGC
47151 TCT
63 T-T
* * *
47154 GTGCATCGGTACACAAAATGCATTCGATATTCAAAATATTCAAGAGTGCATAGATGCATGGCTT
1 GTGCATCGGTGCACAAAATGCATTCGATATTCAAAATATGCAAGAGTGCATAAATGCATGGCTT
47218 GTGCATCGGTGCACAAAATGCATT
1 GTGCATCGGTGCACAAAATGCATT
47242 TGAAATGGGT
Statistics
Matches: 76, Mismatches: 9, Indels: 7
0.83 0.10 0.08
Matches are distributed among these distances:
64 45 0.59
65 31 0.41
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.29
Consensus pattern (64 bp):
GTGCATCGGTGCACAAAATGCATTCGATATTCAAAATATGCAAGAGTGCATAAATGCATGGCTT
Found at i:65772 original size:60 final size:60
Alignment explanation
Indices: 65682--65823 Score: 196
Period size: 60 Copynumber: 2.4 Consensus size: 60
65672 TTGAGTATCT
* * * ** *
65682 AACTATTAAAAGTTATAAACTGATCCCTTAATTATAAGACATTGCTTTGTGAAGTCCTCC
1 AACTACTAAAAGTTACAAAATGATATCTTAATTATAAGACATTGCTTTGTCAAGTCCTCC
* *
65742 GACTATTAAATA-TTACAAAATGATATCTTAATTATAAGACATTGCTTTGTCAAGTCCTCC
1 AACTACTAAA-AGTTACAAAATGATATCTTAATTATAAGACATTGCTTTGTCAAGTCCTCC
65802 AACTACTAAAAGTTACAAAATG
1 AACTACTAAAAGTTACAAAATG
65824 GTAACTCGAC
Statistics
Matches: 72, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
59 1 0.01
60 70 0.97
61 1 0.01
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.34
Consensus pattern (60 bp):
AACTACTAAAAGTTACAAAATGATATCTTAATTATAAGACATTGCTTTGTCAAGTCCTCC
Found at i:68818 original size:68 final size:67
Alignment explanation
Indices: 68736--68908 Score: 188
Period size: 70 Copynumber: 2.5 Consensus size: 67
68726 ATATCGACAT
* * * *
68736 TTTTC-ACAAGTATCGATGCATTTGAATTAAAAATA-TGAAAAATAAGAAAGCTGCAAAGCATCT
1 TTTTCTACAAGTATCGATAC-TTTGAATTAAAAAAATTGAAAAATAAGAAAGCTACAAAGCATCG
68799 ATA
65 ATA
* * * *
68802 CTTTTCTACAAGTATCGATACTTTCGAATTTAAAAAAATTGAAAAATGAGAATGTTACAAAGTAT
1 -TTTTCTACAAGTATCGATACTTT-GAA-TTAAAAAAATTGAAAAATAAGAAAGCTACAAAGCAT
68867 CGATA
63 CGATA
* *
68872 TTTTTTCACAAGTATCAATACTTTTGAATTAAAAAAA
1 TTTTCT-ACAAGTATCGATAC-TTTGAATTAAAAAAA
68909 GCATGGAAAA
Statistics
Matches: 90, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
67 8 0.09
68 16 0.18
69 22 0.24
70 41 0.46
71 3 0.03
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.33
Consensus pattern (67 bp):
TTTTCTACAAGTATCGATACTTTGAATTAAAAAAATTGAAAAATAAGAAAGCTACAAAGCATCGA
TA
Found at i:68863 original size:70 final size:70
Alignment explanation
Indices: 68722--69068 Score: 319
Period size: 71 Copynumber: 4.9 Consensus size: 70
68712 ATAAAAAATT
* * * * *
68722 CAAAATATCGACA-TTTTTCACAAGTATCGATGCATTT-GAA-TT-AAAAATATGAAAAATAAGA
1 CAAAGTATCGATACTTTTTCACAAGTATCGATAC-TTTCGAATTTAAAAAAAATGAAAAATGAGA
*
68783 AAGCTG
65 ATGCTG
* * *
68789 CAAAGCATCTATAC-TTTTCTACAAGTATCGATACTTTCGAATTTAAAAAAATTGAAAAATGAGA
1 CAAAGTATCGATACTTTTTC-ACAAGTATCGATACTTTCGAATTTAAAAAAAATGAAAAATGAGA
* *
68853 ATGTTA
65 ATGCTG
* * * *
68859 CAAAGTATCGATATTTTTTCACAAGTATCAATACTTTTGAA-TTAAAAAAAGCATGGAAAATGAG
1 CAAAGTATCGATACTTTTTCACAAGTATCGATACTTTCGAATTTAAAAAAA--ATGAAAAATGAG
**
68923 AATATTG
64 AATGCTG
* * * * * * *
68930 CAAAGTATCGATAATTTTTCACAAATATCAATACTTTAGAATTTTAAAAAAACTTAGAAAATAAG
1 CAAAGTATCGATACTTTTTCACAAGTATCGATACTTTCGAA-TTTAAAAAAAATGA-AAAATGAG
*
68995 AAGGCTG
64 AATGCTG
* * * *
69002 TAGAGTATCGATACTTTTTCACAAATATTGATACTTTCGAATTTTAAAAAAAAATGAAAAATGAG
1 CAAAGTATCGATACTTTTTCACAAGTATCGATACTTTCGAA-TTT-AAAAAAAATGAAAAATGAG
69067 AA
64 AA
69069 GGATGTAAAT
Statistics
Matches: 229, Mismatches: 39, Indels: 19
0.80 0.14 0.07
Matches are distributed among these distances:
67 17 0.07
68 16 0.07
69 11 0.05
70 49 0.21
71 59 0.26
72 59 0.26
73 18 0.08
ACGTcount: A:0.45, C:0.11, G:0.12, T:0.31
Consensus pattern (70 bp):
CAAAGTATCGATACTTTTTCACAAGTATCGATACTTTCGAATTTAAAAAAAATGAAAAATGAGAA
TGCTG
Found at i:69063 original size:72 final size:70
Alignment explanation
Indices: 68722--69070 Score: 296
Period size: 72 Copynumber: 5.0 Consensus size: 70
68712 ATAAAAAATT
* * * * * * *
68722 CAAAATATCGACA-TTTTTCACAAGTATCGATGCATTT-GAA-TT-AAAAATATGAAAAATAAGA
1 CAAAGTATCGATACTTTTTCACAAATATCAATAC-TTTCGAATTTAAAAAAAATGAAAAATGAGA
*
68783 AAGCTG
65 AGGCTG
* * * * *
68789 CAAAGCATCTATAC-TTTTCTACAAGTATCGATACTTTCGAATTTAAAAAAATTGAAAAATGAGA
1 CAAAGTATCGATACTTTTTC-ACAAATATCAATACTTTCGAATTTAAAAAAAATGAAAAATGAGA
* * *
68853 ATGTTA
65 AGGCTG
* * * *
68859 CAAAGTATCGATATTTTTTCACAAGTATCAATACTTTTGAA-TTAAAAAAAGCATGGAAAATGAG
1 CAAAGTATCGATACTTTTTCACAAATATCAATACTTTCGAATTTAAAAAAA--ATGAAAAATGAG
***
68923 AATATTG
64 AAGGCTG
* * * * *
68930 CAAAGTATCGATAATTTTTCACAAATATCAATACTTTAGAATTTTAAAAAAACTTAGAAAATAAG
1 CAAAGTATCGATACTTTTTCACAAATATCAATACTTTCGAA-TTTAAAAAAAATGA-AAAATGAG
68995 AAGGCTG
64 AAGGCTG
* * **
69002 TAGAGTATCGATACTTTTTCACAAATATTGATACTTTCGAATTTTAAAAAAAAATGAAAAATGAG
1 CAAAGTATCGATACTTTTTCACAAATATCAATACTTTCGAA-TTT-AAAAAAAATGAAAAATGAG
69067 AAGG
64 AAGG
69071 ATGTAAATTA
Statistics
Matches: 231, Mismatches: 39, Indels: 19
0.80 0.13 0.07
Matches are distributed among these distances:
67 17 0.07
68 16 0.07
69 11 0.05
70 49 0.21
71 59 0.26
72 61 0.26
73 18 0.08
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.31
Consensus pattern (70 bp):
CAAAGTATCGATACTTTTTCACAAATATCAATACTTTCGAATTTAAAAAAAATGAAAAATGAGAA
GGCTG
Found at i:69101 original size:71 final size:72
Alignment explanation
Indices: 68931--69101 Score: 177
Period size: 72 Copynumber: 2.4 Consensus size: 72
68921 AGAATATTGC
* * ** * *
68931 AAAGTATCGATAA-TTTTTCACAAATATCAATACTTTAGAATTTTAAAAAAACTTAGAAAATAAG
1 AAAGTATCGA-AACTTTTCCAAAAATATTGATACTTTAGAATTTTAAAAAAAATGAGAAAATAAG
*
68995 AAGGCTGT
65 AAGGATGT
* * * * * *
69003 AGAGTATCGATACTTTTTCACAAATATTGATACTTTCGAATTTTAAAAAAAAATGA-AAAATGAG
1 AAAGTATCGAAACTTTTCCAAAAATATTGATACTTTAGAATTTT-AAAAAAAATGAGAAAATAAG
69067 AAGGATGT
65 AAGGATGT
*
69075 AAATTATC-AAACTTTTCCAAAAATATT
1 AAAGTATCGAAACTTTTCCAAAAATATT
69102 AAAGCATAAG
Statistics
Matches: 83, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
71 17 0.20
72 57 0.69
73 9 0.11
ACGTcount: A:0.46, C:0.10, G:0.11, T:0.33
Consensus pattern (72 bp):
AAAGTATCGAAACTTTTCCAAAAATATTGATACTTTAGAATTTTAAAAAAAATGAGAAAATAAGA
AGGATGT
Found at i:69537 original size:76 final size:77
Alignment explanation
Indices: 69410--69571 Score: 249
Period size: 76 Copynumber: 2.1 Consensus size: 77
69400 TAAACTCTTG
*
69410 TAACA-TTTAGGCGAAACCTAAAATGTTAATAATATTCATAACATTTGTTGTTTATAACTTATTT
1 TAACATTTTAGGCGAAACCTAAAATGTTAATAATATTCATAACATTTATTGTTTATAACTTATTT
*
69474 TCTTAACGTTGA
66 TCCTAACGTTGA
69486 TAACATTTTAGGC-ACAACCTAAAATGTTAA-AATATTCATAACATTTATTGTTTATAACTTATT
1 TAACATTTTAGGCGA-AACCTAAAATGTTAATAATATTCATAACATTTATTGTTTATAACTTATT
* *
69549 TTCCTACCGTTTA
65 TTCCTAACGTTGA
*
69562 TAATATTTTA
1 TAACATTTTA
69572 AATGTAACAT
Statistics
Matches: 79, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
76 57 0.72
77 22 0.28
ACGTcount: A:0.36, C:0.13, G:0.08, T:0.43
Consensus pattern (77 bp):
TAACATTTTAGGCGAAACCTAAAATGTTAATAATATTCATAACATTTATTGTTTATAACTTATTT
TCCTAACGTTGA
Found at i:71687 original size:3 final size:3
Alignment explanation
Indices: 71679--71727 Score: 53
Period size: 3 Copynumber: 15.7 Consensus size: 3
71669 TTTATCTGAG
* * *
71679 TTA TTA TTA TTA TTA TTA TTA TTA TTTA TAA CTA ATA TTA TTA TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA T-TA
71726 TT
1 TT
71728 TTTTTGCAGG
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
3 33 0.85
4 6 0.15
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:81045 original size:23 final size:23
Alignment explanation
Indices: 81019--81066 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
81009 ATAAAGTACA
*
81019 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
81042 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
81065 AT
1 AT
81067 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:81711 original size:331 final size:333
Alignment explanation
Indices: 81106--81771 Score: 1255
Period size: 331 Copynumber: 2.0 Consensus size: 333
81096 TTATACCGAT
81106 AGCATTGCAAATTTACCTATTACATTATATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGA
1 AGCATTGCAAATTTACCTATTACATTATATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGA
*
81171 TCGATATTTCTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTC
66 TCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAA-TTTTTTTAATAGTGTTTCATGTTTTC
*
81236 CACCTACAATATTAATTTAATAATTTTATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTA
130 CACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTA
* *
81301 TAAAATATTATTTAGAATTTTTAATTTAATAATAATATATATCGTAACGTAAAAATAAATCATTA
195 TAAAATAATATTTAGAATTTTTAATTTAATAATAATATATATCGTAACGAAAAAATAAATCATTA
81366 GACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTT
260 GACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTT
81431 TCCACAGTG
325 TCCACAGTG
*
81440 AGCATTGCAAATTTACCTATTATATTATATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGA
1 AGCATTGCAAATTTACCTATTACATTATATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGA
81505 TCGATACTTCTTTTAAAGTTATGTAATTTATGTTTC-A-TTTTTTAATAGTGTTTCATGTTTTCC
66 TCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCC
81568 ACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTAT
131 ACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTAT
81633 AAAATAATATTTAGAATTTTTAATTTAATAATAATATATATCGTAACGAAAAAATAAATCATTAG
196 AAAATAATATTTAGAATTTTTAATTTAATAATAATATATATCGTAACGAAAAAATAAATCATTAG
81698 ACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTT
261 ACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTT
*
81763 TCACAGTG
326 CCACAGTG
81771 A
1 A
81772 AAAAAGTATG
Statistics
Matches: 326, Mismatches: 6, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
331 226 0.69
333 1 0.00
334 99 0.30
ACGTcount: A:0.38, C:0.11, G:0.08, T:0.43
Consensus pattern (333 bp):
AGCATTGCAAATTTACCTATTACATTATATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGA
TCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCC
ACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTAT
AAAATAATATTTAGAATTTTTAATTTAATAATAATATATATCGTAACGAAAAAATAAATCATTAG
ACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTT
CCACAGTG
Found at i:81854 original size:23 final size:23
Alignment explanation
Indices: 81828--81886 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 23
81818 AACCACTACC
81828 TATTACATTATATAAACGATACA
1 TATTACATTATATAAACGATACA
* * *
81851 TATTACATTATATAAGCGCTACC
1 TATTACATTATATAAACGATACA
*
81874 TATTACATCATAT
1 TATTACATTATAT
81887 GTTTACCTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.37
Consensus pattern (23 bp):
TATTACATTATATAAACGATACA
Found at i:82340 original size:39 final size:39
Alignment explanation
Indices: 82286--82372 Score: 147
Period size: 39 Copynumber: 2.2 Consensus size: 39
82276 TCAAGTTGTA
* *
82286 GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGACACCATATGAGATTTG
*
82325 GATTTTGATTTCCTTTTGCTTGACACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGACACCATATGAGATTTG
82364 GATTTTGAT
1 GATTTTGAT
82373 GAGCATCGGA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.18, C:0.14, G:0.20, T:0.48
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTGCTTGACACCATATGAGATTTG
Found at i:82653 original size:18 final size:18
Alignment explanation
Indices: 82630--82666 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
82620 CGAAATATAT
82630 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
82648 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
82666 A
1 A
82667 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:83083 original size:24 final size:25
Alignment explanation
Indices: 83051--83100 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
83041 TTTTTCCAAA
*
83051 TAATGTA-CCATAACAATGTTCAAT
1 TAATGTACCCACAACAATGTTCAAT
*
83075 TAATGTACCCACAACAATGTTTAAT
1 TAATGTACCCACAACAATGTTCAAT
83100 T
1 T
83101 GATTTGTTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 7 0.30
25 16 0.70
ACGTcount: A:0.40, C:0.18, G:0.08, T:0.34
Consensus pattern (25 bp):
TAATGTACCCACAACAATGTTCAAT
Found at i:83387 original size:21 final size:22
Alignment explanation
Indices: 83362--83413 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
83352 ACACTTTACA
*
83362 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
83385 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
83408 ATATAA
1 ATATAA
83414 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:83398 original size:23 final size:23
Alignment explanation
Indices: 83372--83434 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
83362 ATATAACCAC
83372 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
83395 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
83418 TACCTATTACATCATAT
1 TACCTATTACATTATAT
83435 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:83831 original size:25 final size:25
Alignment explanation
Indices: 83774--83839 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
83764 TCACTCAAAG
*
83774 ATGTATATACCTAAATATGTAGTTA
1 ATGTACATACCTAAATATGTAGTTA
***
83799 ACAAACATACCTAAATATGTAGTTA
1 ATGTACATACCTAAATATGTAGTTA
*
83824 TTGTACATACCTAAAT
1 ATGTACATACCTAAAT
83840 TTAATGATAA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.35
Consensus pattern (25 bp):
ATGTACATACCTAAATATGTAGTTA
Found at i:86530 original size:180 final size:181
Alignment explanation
Indices: 86189--86698 Score: 826
Period size: 177 Copynumber: 2.9 Consensus size: 181
86179 TTAAAATTAC
* *
86189 CGATAC-TTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCG-CAC-AT
1 CGATACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
* *
86251 ATTATAAAGTGTCGATATAGGTTGTAGACCTA-TCGCTCATAAACCGTATATTTATACCGGTTAT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAACCGTATATTTATACCGGTTAT
* *
86315 ATTAC-AAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGT
131 ATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
*
86365 CGATACTTTTTTAAATCGTATCGACATATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
1 CGATACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
86430 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAACCGTATATTTATACC-GTTAT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAACCGTATATTTATACCGGTTAT
86494 ATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
131 ATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
86545 CG--ACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
1 CGATACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
86608 ATT-AAAAGTGTCG--ATAGGTTGTAGACCTATTCGCGCATAAAACCGTATATTTATACCGGTTA
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCAT-AAACCGTATATTTATACCGGTTA
* * * **
86670 TATTGCAAATTTACCTATTTTATTATAAT
130 TATTACAAAATTATCTATTACATTATAAT
86699 GTTGAAAGTG
Statistics
Matches: 314, Mismatches: 13, Indels: 13
0.92 0.04 0.04
Matches are distributed among these distances:
175 25 0.08
176 24 0.08
177 86 0.27
178 66 0.21
179 43 0.14
180 70 0.22
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (181 bp):
CGATACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAACCGTATATTTATACCGGTTAT
ATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
Found at i:88145 original size:3 final size:3
Alignment explanation
Indices: 88132--88171 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
88122 TGTTTGGATC
* *
88132 TCA TC- TCA TCA TCA TCA TCA TCA TCG TCA TCA TCT TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
88172 GCCAGCTTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.25, C:0.35, G:0.03, T:0.38
Consensus pattern (3 bp):
TCA
Found at i:88163 original size:18 final size:18
Alignment explanation
Indices: 88132--88222 Score: 85
Period size: 18 Copynumber: 5.1 Consensus size: 18
88122 TGTTTGGATC
*
88132 TCATC-TCATCATCATCA
1 TCATCGTCATCATCATCT
* *
88149 TCATCATCGTCATCATCT
1 TCATCGTCATCATCATCT
* * * *
88167 TCATCGCCAGCTTCATCG
1 TCATCGTCATCATCATCT
*
88185 TCATCGTCATCGTCATCT
1 TCATCGTCATCATCATCT
* *
88203 TCATCGTCAGCTTCATCT
1 TCATCGTCATCATCATCT
88221 TC
1 TC
88223 TGCGACCGCT
Statistics
Matches: 59, Mismatches: 14, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
17 5 0.08
18 54 0.92
ACGTcount: A:0.20, C:0.35, G:0.09, T:0.36
Consensus pattern (18 bp):
TCATCGTCATCATCATCT
Found at i:88180 original size:12 final size:12
Alignment explanation
Indices: 88165--88219 Score: 74
Period size: 12 Copynumber: 4.6 Consensus size: 12
88155 TCGTCATCAT
*
88165 CTTCATCGCCAG
1 CTTCATCGTCAG
*
88177 CTTCATCGTCAT
1 CTTCATCGTCAG
* *
88189 CGTCATCGTCAT
1 CTTCATCGTCAG
88201 CTTCATCGTCAG
1 CTTCATCGTCAG
88213 CTTCATC
1 CTTCATC
88220 TTCTGCGACC
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 38 1.00
ACGTcount: A:0.16, C:0.36, G:0.13, T:0.35
Consensus pattern (12 bp):
CTTCATCGTCAG
Found at i:88222 original size:6 final size:6
Alignment explanation
Indices: 88132--88211 Score: 63
Period size: 6 Copynumber: 13.5 Consensus size: 6
88122 TGTTTGGATC
* * * * * * * * *
88132 TCATC- TCATCA TCATCA TCATCA TCGTCA TCATCT TCATCG CCAGCT
1 TCATCG TCATCG TCATCG TCATCG TCATCG TCATCG TCATCG TCATCG
*
88179 TCATCG TCATCG TCATCG TCATCT TCATCG TCA
1 TCATCG TCATCG TCATCG TCATCG TCATCG TCA
88212 GCTTCATCTT
Statistics
Matches: 62, Mismatches: 12, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
5 5 0.08
6 57 0.92
ACGTcount: A:0.21, C:0.35, G:0.09, T:0.35
Consensus pattern (6 bp):
TCATCG
Done.