Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005624.1 Hibiscus syriacus cultivar Beakdansim tig00013095_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: 116385
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:4530 original size:18 final size:18
Alignment explanation
Indices: 4488--4530 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 18
4478 AATCTACAAC
4488 AAATTTCATCAAAAACAT
1 AAATTTCATCAAAAACAT
4506 AAGATTTC-TCAAAAACATT
1 AA-ATTTCATCAAAAACA-T
4525 AAATTT
1 AAATTT
4531 TTTTAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 15 0.65
19 8 0.35
ACGTcount: A:0.51, C:0.14, G:0.02, T:0.33
Consensus pattern (18 bp):
AAATTTCATCAAAAACAT
Found at i:16836 original size:13 final size:13
Alignment explanation
Indices: 16818--16843 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
16808 ATCTTATCAG
16818 TCAGCTCCATGGA
1 TCAGCTCCATGGA
16831 TCAGCTCCATGGA
1 TCAGCTCCATGGA
16844 GTTTGAGCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.31, G:0.23, T:0.23
Consensus pattern (13 bp):
TCAGCTCCATGGA
Found at i:18485 original size:18 final size:20
Alignment explanation
Indices: 18444--18481 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
18434 TTTCGTGCAC
* *
18444 CAATTTGATTTTTTCTTTGT
1 CAATATGATTTTATCTTTGT
18464 CAATATGATTTTATCTTT
1 CAATATGATTTTATCTTT
18482 CAATTTGTTT
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:0.11, G:0.08, T:0.61
Consensus pattern (20 bp):
CAATATGATTTTATCTTTGT
Found at i:18793 original size:26 final size:27
Alignment explanation
Indices: 18738--18801 Score: 76
Period size: 26 Copynumber: 2.4 Consensus size: 27
18728 ATTTTCAAGT
*
18738 ATGTTTTAAAATGTGATATGTTGATAG
1 ATGTTTTAAAATGTGAAATGTTGATAG
* * *
18765 ATGTTTTAATATG-GAAATGTTTATGG
1 ATGTTTTAAAATGTGAAATGTTGATAG
18791 ATGTTTCTAAA
1 ATGTTT-TAAA
18802 TATTGCTAGT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
26 16 0.52
27 15 0.48
ACGTcount: A:0.33, C:0.02, G:0.20, T:0.45
Consensus pattern (27 bp):
ATGTTTTAAAATGTGAAATGTTGATAG
Found at i:18986 original size:23 final size:23
Alignment explanation
Indices: 18954--19011 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
18944 AGAACGTTAT
*
18954 ACGAATGCTAAACAAACATGTTC
1 ACGAACGCTAAACAAACATGTTC
* *
18977 GCGAACGCTAAACGAACATGTTC
1 ACGAACGCTAAACAAACATGTTC
*
19000 ACGAACGTTAAA
1 ACGAACGCTAAA
19012 TGAAGGCTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.41, C:0.22, G:0.17, T:0.19
Consensus pattern (23 bp):
ACGAACGCTAAACAAACATGTTC
Found at i:19006 original size:57 final size:57
Alignment explanation
Indices: 18911--19069 Score: 165
Period size: 57 Copynumber: 2.8 Consensus size: 57
18901 AACATTTTTG
* * * * * *
18911 AACATGTTCGCGAAAGTTAAACAAACCTGTCCAAGAACGTTATACGAATGCTAAACA
1 AACATGTTCGCGAACGTTAAACAAACATGTTCACGAACGTTAAACGAAGGCTAAACA
* * * *
18968 AACATGTTCGCGAACGCTAAACGAACATGTTCACGAACGTTAAATGAAGGCTAAACG
1 AACATGTTCGCGAACGTTAAACAAACATGTTCACGAACGTTAAACGAAGGCTAAACA
* * * * * *
19025 AACACGTTCGTGAACATTTAAACTAACATGTTCACGGACATTAAA
1 AACATGTTCGCGAAC-GTTAAACAAACATGTTCACGAACGTTAAA
19070 TGAACACGTT
Statistics
Matches: 84, Mismatches: 17, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
57 60 0.71
58 24 0.29
ACGTcount: A:0.40, C:0.21, G:0.17, T:0.22
Consensus pattern (57 bp):
AACATGTTCGCGAACGTTAAACAAACATGTTCACGAACGTTAAACGAAGGCTAAACA
Found at i:19046 original size:24 final size:23
Alignment explanation
Indices: 19019--19092 Score: 76
Period size: 23 Copynumber: 3.2 Consensus size: 23
19009 AAATGAAGGC
*
19019 TAAACGAACACGTTCGTGAACATT
1 TAAACGAACACGTTCGCGAACA-T
* * * *
19043 TAAACTAACATGTTCACGGACAT
1 TAAACGAACACGTTCGCGAACAT
* *
19066 TAAATGAACACGTTCGCGAATAT
1 TAAACGAACACGTTCGCGAACAT
19089 TAAA
1 TAAA
19093 TGAATGAACA
Statistics
Matches: 39, Mismatches: 11, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
23 22 0.56
24 17 0.44
ACGTcount: A:0.41, C:0.19, G:0.15, T:0.26
Consensus pattern (23 bp):
TAAACGAACACGTTCGCGAACAT
Found at i:19108 original size:14 final size:14
Alignment explanation
Indices: 19089--19116 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
19079 TCGCGAATAT
19089 TAAATGAATGAACA
1 TAAATGAATGAACA
19103 TAAATGAATGAACA
1 TAAATGAATGAACA
19117 CGAACACTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.14, T:0.21
Consensus pattern (14 bp):
TAAATGAATGAACA
Found at i:24490 original size:3 final size:3
Alignment explanation
Indices: 24482--24506 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
24472 ACTAATTTTG
24482 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
24507 CTAGAATCAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:29107 original size:2 final size:2
Alignment explanation
Indices: 29100--29124 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
29090 ACTACTACTT
29100 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 T
29125 TTCCACAACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:30423 original size:21 final size:21
Alignment explanation
Indices: 30399--30469 Score: 99
Period size: 21 Copynumber: 3.4 Consensus size: 21
30389 ATTTTTTACC
*
30399 TATTTTTATTATTATTGATA-T
1 TATTATTATTATTATT-ATATT
*
30420 TATTATTATTATTATTTTATT
1 TATTATTATTATTATTATATT
*
30441 TATTATTATTATTATTAAATT
1 TATTATTATTATTATTATATT
30462 TATTATTA
1 TATTATTA
30470 CAAACAGGCT
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
20 2 0.04
21 43 0.96
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.66
Consensus pattern (21 bp):
TATTATTATTATTATTATATT
Found at i:30464 original size:12 final size:11
Alignment explanation
Indices: 30407--30469 Score: 53
Period size: 12 Copynumber: 5.8 Consensus size: 11
30397 CCTATTTTTA
*
30407 TTATTATTGAT
1 TTATTATTAAT
30418 ATTATTATT-A-
1 -TTATTATTAAT
*
30428 TTATTATTTTAT
1 TTATTA-TTAAT
30440 TTATTATT-A-
1 TTATTATTAAT
30449 TTATTATTAAAT
1 TTATTATT-AAT
30461 TTATTATTA
1 TTATTATTA
30470 CAAACAGGCT
Statistics
Matches: 45, Mismatches: 0, Indels: 13
0.78 0.00 0.22
Matches are distributed among these distances:
9 14 0.31
10 3 0.07
11 6 0.13
12 22 0.49
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (11 bp):
TTATTATTAAT
Found at i:30469 original size:3 final size:3
Alignment explanation
Indices: 30399--30457 Score: 77
Period size: 3 Copynumber: 19.7 Consensus size: 3
30389 ATTTTTTACC
*
30399 TAT TTT TAT TAT TAT TGA- TAT TAT TAT TAT TAT TAT T-T TATT TAT
1 TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TA-T TAT
30444 TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TA
30458 AATTTATTAT
Statistics
Matches: 50, Mismatches: 2, Indels: 8
0.83 0.03 0.13
Matches are distributed among these distances:
2 3 0.06
3 43 0.86
4 4 0.08
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:32068 original size:20 final size:19
Alignment explanation
Indices: 32043--32084 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
32033 TTATTTTATA
32043 AATTATATATTAATTGTTTT
1 AATTATATATTAATT-TTTT
* *
32063 AATTATTTATTTATTTTTT
1 AATTATATATTAATTTTTT
32082 AAT
1 AAT
32085 ATCGAAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
AATTATATATTAATTTTTT
Found at i:32079 original size:118 final size:117
Alignment explanation
Indices: 31940--32175 Score: 318
Period size: 120 Copynumber: 2.0 Consensus size: 117
31930 ATTTTAATCA
* * * *
31940 TGTTTTAATATTTATTTA-TTTTCAATAT-TAAG-AAAG-GGTAGTCTTAAAACAACTGGATGTC
1 TGTTTTAATATTTATTTATTTTTCAATATCGAAGAAAAGAGCTA-TCTTAAAACAACTAGAAGT-
*
32001 CATTTTCTGATATTTTTAAATAAATAAATATCTTATTTTATAAATTATATATTAAT
64 CATTTTCTGATATTTTTAAATAAATAAATATCTTA-TTTATAAATT-TATATAAAT
* * *
32057 TGTTTTAATTATTTATTTATTTTTTAATATCGAAGAAAAGAGCTATCTTAAGACACCTAGAAGTC
1 TGTTTTAA-TATTTATTTATTTTTCAATATCGAAGAAAAGAGCTATCTTAAAACAACTAGAAGTC
*
32122 ATTTTCTGATATTTTTAAATAAATAAATATTTTATTTATAAATTTATATAAAT
65 ATTTTCTGATATTTTTAAATAAATAAATATCTTATTTATAAATTTATATAAAT
32175 T
1 T
32176 AATAAATTTA
Statistics
Matches: 105, Mismatches: 9, Indels: 9
0.85 0.07 0.07
Matches are distributed among these distances:
117 8 0.08
118 19 0.18
119 19 0.18
120 37 0.35
121 19 0.18
122 3 0.03
ACGTcount: A:0.38, C:0.07, G:0.08, T:0.47
Consensus pattern (117 bp):
TGTTTTAATATTTATTTATTTTTCAATATCGAAGAAAAGAGCTATCTTAAAACAACTAGAAGTCA
TTTTCTGATATTTTTAAATAAATAAATATCTTATTTATAAATTTATATAAAT
Found at i:34251 original size:8 final size:7
Alignment explanation
Indices: 34227--34268 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
34217 TTTTCATACA
34227 TGCA-TT
1 TGCATTT
34233 TGCATTT
1 TGCATTT
34240 TGCATCTT
1 TGCAT-TT
34248 TGCATTT
1 TGCATTT
* *
34255 TTCATTG
1 TGCATTT
34262 TGCATTT
1 TGCATTT
34269 ATACTTTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
6 4 0.13
7 19 0.63
8 7 0.23
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (7 bp):
TGCATTT
Found at i:34251 original size:15 final size:14
Alignment explanation
Indices: 34227--34268 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
34217 TTTTCATACA
34227 TGCA-TTTGCATTT
1 TGCATTTTGCATTT
34240 TGCATCTTTGCATTT
1 TGCAT-TTTGCATTT
* *
34255 TTCATTGTGCATTT
1 TGCATTTTGCATTT
34269 ATACTTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 4 0.16
14 8 0.32
15 13 0.52
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (14 bp):
TGCATTTTGCATTT
Found at i:35994 original size:2 final size:2
Alignment explanation
Indices: 35987--36048 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
35977 ATCCTTTTAA
35987 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
36029 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
36049 CATTTGTTGT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:36371 original size:11 final size:11
Alignment explanation
Indices: 36357--36390 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
36347 AAGAAGAAGG
36357 AAAAAAAAG-A
1 AAAAAAAAGAA
36367 AAAAAAAAGAA
1 AAAAAAAAGAA
*
36378 AAAAAAAGGAA
1 AAAAAAAAGAA
36389 AA
1 AA
36391 TTGAATCAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 9 0.41
11 13 0.59
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGAA
Found at i:36372 original size:10 final size:10
Alignment explanation
Indices: 36342--36390 Score: 62
Period size: 10 Copynumber: 4.8 Consensus size: 10
36332 CTCATCCAGT
*
36342 AAAGAAAGAA
1 AAAGAAAAAA
* *
36352 GAAGGAAAAA
1 AAAGAAAAAA
36362 AAAGAAAAAA
1 AAAGAAAAAA
36372 AAAGAAAAAA
1 AAAGAAAAAA
36382 AAAGGAAAA
1 AAA-GAAAA
36391 TTGAATCAAG
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
10 28 0.85
11 5 0.15
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (10 bp):
AAAGAAAAAA
Found at i:38858 original size:114 final size:114
Alignment explanation
Indices: 38657--38880 Score: 385
Period size: 114 Copynumber: 2.0 Consensus size: 114
38647 GTTCCACGTT
*
38657 CTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATATG
1 CTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATATG
* * *
38722 GTTTGGTATGAACCCCAAAACCAATCATTAGATTTGAAAGATGAATTTG
66 GTTCGGTAGGAACCCCAAAACCAATCATTAGAATTGAAAGATGAATTTG
*
38771 CTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTG
1 CTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATATG
* *
38836 GTTCGGTAGGAACCCCAGAACCAATCATTGGAATTGAAAGATGAA
66 GTTCGGTAGGAACCCCAAAACCAATCATTAGAATTGAAAGATGAA
38881 CTGCATGATC
Statistics
Matches: 103, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
114 103 1.00
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.29
Consensus pattern (114 bp):
CTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATATG
GTTCGGTAGGAACCCCAAAACCAATCATTAGAATTGAAAGATGAATTTG
Found at i:41564 original size:22 final size:22
Alignment explanation
Indices: 41538--41617 Score: 115
Period size: 22 Copynumber: 3.6 Consensus size: 22
41528 TACATCTACA
41538 CTCTTCAAAGATGATAGATTCT
1 CTCTTCAAAGATGATAGATTCT
*
41560 CTCTTCAAAGATGATAAATTCT
1 CTCTTCAAAGATGATAGATTCT
* *
41582 CTTTTTAAAGATGATAGATTCT
1 CTCTTCAAAGATGATAGATTCT
* *
41604 CTTTTCGAAGATGA
1 CTCTTCAAAGATGA
41618 AAGCTTTATT
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 52 1.00
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.39
Consensus pattern (22 bp):
CTCTTCAAAGATGATAGATTCT
Found at i:42572 original size:113 final size:113
Alignment explanation
Indices: 42364--43225 Score: 1207
Period size: 113 Copynumber: 7.7 Consensus size: 113
42354 TTCCAGAAGG
* * *
42364 GTTCATAATGAGAAGAACTCATATGAAGAAGGAAAAAGAAATTCATAATGAGAAGAGCTTGTTCA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCA
*
42429 ACCTTTTGCTCAAATCCATCACTCGATGGATCAACTTTTCCAGAGAAA
66 ACCTTTTGCTTAAATCCATCACTCGATGGATCAACTTTTCCAGAGAAA
**
42477 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCA
* * * * ** * * *
42542 ACCTTTTGTTTGAATTCATC-GTTTACTGGATCAACATTGCCAG-GTAGA
66 ACCTTTTGCTTAAATCCATCACTCGA-TGGATCAACTTTTCCAGAG-AAA
*
42590 GTTCATAATGAGAAGAACTCTTCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCA
*
42655 ACCTTTTGCTCAAATCCATCACTCGATGGATCAACTTTTCCAGAGAAA
66 ACCTTTTGCTTAAATCCATCACTCGATGGATCAACTTTTCCAGAGAAA
*
42703 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTAA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCA
* * *
42768 ACCTTTTGCTCAAAT-C--CACTTGATGGATCAGCTTTTCCAGAGAAA
66 ACCTTTTGCTTAAATCCATCACTCGATGGATCAACTTTTCCAGAGAAA
*
42813 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAATAAGTTCATAATGAGAAGAGCTTGTTCA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCA
*
42878 ACCTTTTGCTTAAATCCATCACTCGATGGATCAACTTTTCCAGAGATA
66 ACCTTTTGCTTAAATCCATCACTCGATGGATCAACTTTTCCAGAGAAA
* * **
42926 GTTCATAATGAGAAGAACTCATCTGAAAAAGGAATAAGAAGTTCATAATGAGAAGAATTTGTTCA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCA
* * * * * * * *
42991 ACCTTTTGTTTGAATTCATCATTTGATGGATCAACATTGCCAG-GTAGA
66 ACCTTTTGCTTAAATCCATCACTCGATGGATCAACTTTTCCAGAG-AAA
* * * * **
43039 GTTCATAATGAGAAGAAATCGTTTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCA
* * *
43104 A-CTTTTAGTTTGAATTCATCACTCGATGGATCAACTTTTCCAGAGAAA
66 ACCTTTT-GCTTAAATCCATCACTCGATGGATCAACTTTTCCAGAGAAA
* * * *
43152 GTTCATAATGAGAATAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAAAAGAGCTTGTTCG
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCA
43217 ACCTTTTGC
66 ACCTTTTGC
43226 ATGACTCTAT
Statistics
Matches: 665, Mismatches: 73, Indels: 22
0.88 0.10 0.03
Matches are distributed among these distances:
110 104 0.16
111 1 0.00
112 10 0.02
113 541 0.81
114 9 0.01
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.28
Consensus pattern (113 bp):
GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCA
ACCTTTTGCTTAAATCCATCACTCGATGGATCAACTTTTCCAGAGAAA
Found at i:43210 original size:449 final size:449
Alignment explanation
Indices: 42364--43225 Score: 1478
Period size: 449 Copynumber: 1.9 Consensus size: 449
42354 TTCCAGAAGG
42364 GTTCATAATGAGAAGAACTCATATGAAGAAGGAAAAAGAAATTCATAATGAGAAGAGCTTGTTCA
1 GTTCATAATGAGAAGAACTCATATGAAGAAGGAAAAAGAAATTCATAATGAGAAGAGCTTGTTCA
42429 ACCTTTTGCTCAAATCCATCACTCGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAA
66 ACCTTTTGCTCAAATCCATCACTCGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAA
*
42494 CTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATTC
131 CTCATCTGAAAAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATTC
* *
42559 ATCGTTTACTGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCTTCTGAAGAAGGAA
196 ATCATTTACTGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAAATCTTCTGAAGAAGGAA
* *
42624 GAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAATCCATCACTCGATGGATCAA
261 GAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCACTCGATGGATCAA
*
42689 CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
326 CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAA
*
42754 GAAGAGCTTGTTAAACCTTTTGCTCAAATCCACTTGATGGATCAGCTTTTCCAGAGAAA
391 AAAGAGCTTGTTAAACCTTTTGCTCAAATCCACTTGATGGATCAGCTTTTCCAGAGAAA
* * * *
42813 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAATAAGTTCATAATGAGAAGAGCTTGTTCA
1 GTTCATAATGAGAAGAACTCATATGAAGAAGGAAAAAGAAATTCATAATGAGAAGAGCTTGTTCA
* *
42878 ACCTTTTGCTTAAATCCATCACTCGATGGATCAACTTTTCCAGAGATAGTTCATAATGAGAAGAA
66 ACCTTTTGCTCAAATCCATCACTCGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAA
*
42943 CTCATCTGAAAAAGGAATAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATTC
131 CTCATCTGAAAAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATTC
43008 ATCATTTGA-TGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAAATCGTT-TGAAGAAGG
196 ATCATTT-ACTGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAAATC-TTCTGAAGAAGG
* * ** *
43071 AAGAAGAAATTCATAATGAGAAGAATTTGTTCAA-CTTTTAGTTTGAATTCATCACTCGATGGAT
259 AAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTT-GCTCAAATCCATCACTCGATGGAT
*
43135 CAACTTTTCCAGAGAAAGTTCATAATGAGAATAACTCATCTGAAGAAGGAAGAAGAAGTTCATAA
323 CAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAA
**
43200 TAAAAAGAGCTTGTTCGACCTTTTGC
388 TAAAAAGAGCTTGTTAAACCTTTTGC
43226 ATGACTCTAT
Statistics
Matches: 388, Mismatches: 22, Indels: 6
0.93 0.05 0.01
Matches are distributed among these distances:
448 5 0.01
449 380 0.98
450 3 0.01
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.28
Consensus pattern (449 bp):
GTTCATAATGAGAAGAACTCATATGAAGAAGGAAAAAGAAATTCATAATGAGAAGAGCTTGTTCA
ACCTTTTGCTCAAATCCATCACTCGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAA
CTCATCTGAAAAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATTC
ATCATTTACTGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAAATCTTCTGAAGAAGGAA
GAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCACTCGATGGATCAA
CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAA
AAAGAGCTTGTTAAACCTTTTGCTCAAATCCACTTGATGGATCAGCTTTTCCAGAGAAA
Found at i:43238 original size:113 final size:113
Alignment explanation
Indices: 42364--43342 Score: 1162
Period size: 113 Copynumber: 8.6 Consensus size: 113
42354 TTCCAGAAGG
* * *
42364 GTTCATAATGAGAAGAACTCATATGAAGAAGGAAAAAGAAATTCATAATGAGAAGAGCTTGTTCA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCA
** *
42429 ACCTTTTGCTCAAATCCATCACTCGATGGATCAACTTTTCCAGAGAAA
66 ACCTTTTGCTTGAATCTATCACTCGATGGATCAACTTTTCCAGAGAAA
**
42477 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCA
* * ** * * *
42542 ACCTTTTGTTTGAAT-TCATC-GTTTACTGGATCAACATTGCCAG-GTAGA
66 ACCTTTTGCTTGAATCT-ATCACTCGA-TGGATCAACTTTTCCAGAG-AAA
*
42590 GTTCATAATGAGAAGAACTCTTCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCA
** *
42655 ACCTTTTGCTCAAATCCATCACTCGATGGATCAACTTTTCCAGAGAAA
66 ACCTTTTGCTTGAATCTATCACTCGATGGATCAACTTTTCCAGAGAAA
*
42703 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTAA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCA
** * *
42768 ACCTTTTGCTCAAATC---CACTTGATGGATCAGCTTTTCCAGAGAAA
66 ACCTTTTGCTTGAATCTATCACTCGATGGATCAACTTTTCCAGAGAAA
*
42813 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAATAAGTTCATAATGAGAAGAGCTTGTTCA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCA
* * *
42878 ACCTTTTGCTTAAATCCATCACTCGATGGATCAACTTTTCCAGAGATA
66 ACCTTTTGCTTGAATCTATCACTCGATGGATCAACTTTTCCAGAGAAA
* * **
42926 GTTCATAATGAGAAGAACTCATCTGAAAAAGGAATAAGAAGTTCATAATGAGAAGAATTTGTTCA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCA
* * * * * *
42991 ACCTTTTGTTTGAAT-TCATCATTTGATGGATCAACATTGCCAG-GTAGA
66 ACCTTTTGCTTGAATCT-ATCACTCGATGGATCAACTTTTCCAGAG-AAA
* * * * **
43039 GTTCATAATGAGAAGAAATCGTTTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCA
*
43104 A-CTTTTAGTTTGAAT-TCATCACTCGATGGATCAACTTTTCCAGAGAAA
66 ACCTTTT-GCTTGAATCT-ATCACTCGATGGATCAACTTTTCCAGAGAAA
* * * *
43152 GTTCATAATGAGAATAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAAAAGAGCTTGTTCG
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCA
* * * * * *
43217 ACCTTTTGCATGACTCTATCAC-AGAAGGAGATATATTATCATCAGTATTTCCAGA-AGGA
66 ACCTTTTGCTTGAATCTATCACTCG-ATG-G-------ATCA--ACT-TTTCCAGAGA-AA
*
43276 GTTCATAATGAGAAGAACTCATCT---GAA-GAAGAAGAAGTTCACAATGAGAAGAGCTTGTTCA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCA
43337 ACCTTT
66 ACCTTT
43343 GCTAGATTAC
Statistics
Matches: 754, Mismatches: 84, Indels: 49
0.85 0.09 0.06
Matches are distributed among these distances:
110 105 0.14
112 10 0.01
113 550 0.73
114 11 0.01
120 36 0.05
121 7 0.01
123 3 0.00
124 32 0.04
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.28
Consensus pattern (113 bp):
GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCA
ACCTTTTGCTTGAATCTATCACTCGATGGATCAACTTTTCCAGAGAAA
Found at i:43579 original size:3 final size:3
Alignment explanation
Indices: 43571--43617 Score: 60
Period size: 3 Copynumber: 15.7 Consensus size: 3
43561 TTTTTATTGA
* *
43571 TAT TAT TAT TAT TAT T-T TATT TAT TAT TAT TAT TAA AAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT
43616 TA
1 TA
43618 CAAACATGTC
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
2 2 0.05
3 33 0.87
4 3 0.08
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:45227 original size:20 final size:19
Alignment explanation
Indices: 45202--45243 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
45192 CTATTTTATA
45202 AATTATATATTAATTGTTTT
1 AATTATATATTAATT-TTTT
* *
45222 AATTATTTATTTATTTTTT
1 AATTATATATTAATTTTTT
45241 AAT
1 AAT
45244 ATCGAAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
AATTATATATTAATTTTTT
Found at i:45234 original size:119 final size:117
Alignment explanation
Indices: 45098--45334 Score: 309
Period size: 120 Copynumber: 2.0 Consensus size: 117
45088 ATTTTAATCC
* * * *
45098 TGTTTTAATATTTATTTATTTTTCAATAT-TAAG-AAAGAGC-AGTCTTAAAATAACTGGATGTC
1 TGTTTTAATATTTATTTATTTTTCAATATCGAAGAAAAGAGCTA-TCTTAAAACAACTAGAAGT-
*
45160 CATTTTCTGATATTTTTAAATAAATAAATATCCTATTTTATAAATTATATATTAAT
64 CATTTTCTGATATTTTTAAATAAATAAATATCCTA-TTTATAAATT-TATATAAAT
* ** *
45216 TGTTTTAATTATTTATTTATTTTTTAATATCGAAGAAAAGAGCTATCTTAAGGCACCTAGAAGTC
1 TGTTTTAA-TATTTATTTATTTTTCAATATCGAAGAAAAGAGCTATCTTAAAACAACTAGAAGTC
**
45281 ATTTTCTGATATTTTTAAATAAATAAATATTTTATTTATAAATTTATATAAAT
65 ATTTTCTGATATTTTTAAATAAATAAATATCCTATTTATAAATTTATATAAAT
45334 T
1 T
45335 AATAAATTTA
Statistics
Matches: 104, Mismatches: 11, Indels: 8
0.85 0.09 0.07
Matches are distributed among these distances:
118 17 0.16
119 30 0.29
120 36 0.35
121 20 0.19
122 1 0.01
ACGTcount: A:0.38, C:0.07, G:0.08, T:0.47
Consensus pattern (117 bp):
TGTTTTAATATTTATTTATTTTTCAATATCGAAGAAAAGAGCTATCTTAAAACAACTAGAAGTCA
TTTTCTGATATTTTTAAATAAATAAATATCCTATTTATAAATTTATATAAAT
Found at i:46601 original size:31 final size:32
Alignment explanation
Indices: 46565--46636 Score: 92
Period size: 31 Copynumber: 2.2 Consensus size: 32
46555 TTATTTTGAT
* * *
46565 TTTGCCTCCCTCATTTTATATGGTTAA-ATAC
1 TTTGCCCCCCACATTTTATATGATTAATATAC
*
46596 TTTGCCCCCCACATTTTTTATGATTAATTATAC
1 TTTGCCCCCCACATTTTATATGATTAA-TATAC
46629 TTTGCCCC
1 TTTGCCCC
46637 TTAAGTTGGA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 23 0.66
33 12 0.34
ACGTcount: A:0.21, C:0.26, G:0.08, T:0.44
Consensus pattern (32 bp):
TTTGCCCCCCACATTTTATATGATTAATATAC
Found at i:48329 original size:6 final size:6
Alignment explanation
Indices: 48318--48378 Score: 95
Period size: 6 Copynumber: 10.2 Consensus size: 6
48308 GACACGTATT
* * *
48318 ACCACG ACCACG ACCACG ACCACG ACCTCG ACCTCG ACCTCG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
48366 ACCACG ACCACG A
1 ACCACG ACCACG A
48379 GCCGAGCCGA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 53 1.00
ACGTcount: A:0.30, C:0.49, G:0.16, T:0.05
Consensus pattern (6 bp):
ACCACG
Found at i:48386 original size:5 final size:5
Alignment explanation
Indices: 48376--48424 Score: 62
Period size: 5 Copynumber: 9.8 Consensus size: 5
48366 ACCACGACCA
* * * *
48376 CGAGC CGAGC CGAGC CGAGC CGTGC CGTGC CGTGC CGAGC CGAGA CGAG
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAG
48425 ACGGACGGAC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 41 1.00
ACGTcount: A:0.16, C:0.37, G:0.41, T:0.06
Consensus pattern (5 bp):
CGAGC
Found at i:54300 original size:6 final size:6
Alignment explanation
Indices: 54289--54373 Score: 134
Period size: 6 Copynumber: 14.2 Consensus size: 6
54279 GACACGTATT
*
54289 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCTCG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
* * *
54337 ACCTCG ACCTCG ACCTCG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A
54374 GCCGAGCCGA
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 77 1.00
ACGTcount: A:0.29, C:0.49, G:0.16, T:0.05
Consensus pattern (6 bp):
ACCACG
Found at i:54381 original size:5 final size:5
Alignment explanation
Indices: 54371--54424 Score: 72
Period size: 5 Copynumber: 10.8 Consensus size: 5
54361 ACCACGACCA
* * * *
54371 CGAGC CGAGC CGAGC CGAGC CGAGC CGTGC CGTGC CGTGC CGAGC CGAGA
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC
54421 CGAG
1 CGAG
54425 ACGGACGGAC
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 46 1.00
ACGTcount: A:0.17, C:0.37, G:0.41, T:0.06
Consensus pattern (5 bp):
CGAGC
Found at i:90409 original size:21 final size:22
Alignment explanation
Indices: 90383--90442 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 22
90373 CAGAACCTCT
90383 AGGGGGTATCGATTCCCCTAC-
1 AGGGGGTATCGATTCCCCTACA
* * *
90404 AGGGGG-AGTTGGTTCCCCTTCA
1 AGGGGGTA-TCGATTCCCCTACA
*
90426 AGGGGGTATCTATTCCC
1 AGGGGGTATCGATTCCC
90443 TCTGCACCAA
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
20 1 0.03
21 16 0.53
22 12 0.40
23 1 0.03
ACGTcount: A:0.17, C:0.25, G:0.32, T:0.27
Consensus pattern (22 bp):
AGGGGGTATCGATTCCCCTACA
Found at i:94301 original size:20 final size:20
Alignment explanation
Indices: 94259--94301 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
94249 TTATTTTCAT
* *
94259 TTTTTAATTTTGAAACATCA
1 TTTTTAATTTTGAAAAATAA
94279 TTTTTATATTTT-AAAAATAA
1 TTTTTA-ATTTTGAAAAATAA
94299 TTT
1 TTT
94302 CTCATAATCC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (20 bp):
TTTTTAATTTTGAAAAATAA
Found at i:109982 original size:31 final size:31
Alignment explanation
Indices: 109912--109983 Score: 78
Period size: 32 Copynumber: 2.3 Consensus size: 31
109902 ATATTTTTGG
* *
109912 TTTTAA-AAATTTTAAATATTAATCTTAAGT
1 TTTTAATAATTTTTAAATATTAATATTAAGT
109942 TTTTAAATAATTTTTGAAATATTAAATATT-A-T
1 TTTT-AATAATTTTT-AAATATT-AATATTAAGT
109974 TTTTAATAAT
1 TTTTAATAAT
109984 AATAAAATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
30 4 0.11
31 8 0.22
32 11 0.31
33 8 0.22
34 5 0.14
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (31 bp):
TTTTAATAATTTTTAAATATTAATATTAAGT
Found at i:113315 original size:16 final size:17
Alignment explanation
Indices: 113289--113324 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
113279 GGCTAATTTA
*
113289 GTTTCCTAGCTGTTATT
1 GTTTCCTAGCTGTAATT
113306 GTTT-CTAGCTGTAATT
1 GTTTCCTAGCTGTAATT
113322 GTT
1 GTT
113325 ATTATTGGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.14, C:0.14, G:0.19, T:0.53
Consensus pattern (17 bp):
GTTTCCTAGCTGTAATT
Done.