Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008471.1 Hibiscus syriacus cultivar Beakdansim tig00111297_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: 50258
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:4730 original size:230 final size:221
Alignment explanation
Indices: 4381--4846 Score: 654
Period size: 229 Copynumber: 2.1 Consensus size: 221
4371 TGAATTAGAA
4381 ACCCGACCCGACCCGAAATAATAAAAAAACTATTTTTATTCAATAAAAACAGTGACTTAATTGGA
1 ACCCGACCCGACCCGAAATAATAAAAAAACTATTTTTATTCAATAAAAACAGTGACTTAATTGGA
* *
4446 ATAACAATATATATAGATGGGTATTATTGTAATTATTCCTAAATATATAGGTAAAATTATACATT
66 ATAAAAATATATATAGAGGGGTATTATTGTAATTATTCCTAAATATATAGGTAAAATTAT--A-T
* * *
4511 TTTTGGTTCGAGTGGGGTCGGGTATTTTTCACCCTAAACCCGAACCCGACCCGA-ATATCA-CAC
128 ATAT--TTC-----GGGTCGGGTATTTTTCACCCTAAACCCGAACCCGACCCGACAAAT-ATCAC
* *
4574 TTAAAAAAA-TGACCTGACCCGACCAAAATAAAGTTT
185 TTAAAAAAACCGACCCGACCCGACCAAAATAAAGTTT
*
4610 CACCCGACCCGACCCGAAATAATAAAAAAATTATTTTTATTCAAT-AAAACAGTGACTTAATTGG
1 -ACCCGACCCGACCCGAAATAATAAAAAAACTATTTTTATTCAATAAAAACAGTGACTTAATTGG
*
4674 AA-AAAAATTATATATAGAGGGGTATTATTGTAATTATTCCTGAATATATAAGGTAAAATTATAT
65 AATAAAAA-TATATATAGAGGGGTATTATTGTAATTATTCCTAAATATAT-AGGTAAAATTATAT
* *
4738 ATATTTCGGGTCGGGTATTTTTCACCCTAAACCCGAACTCGACCCGACCCAAATATTACTTAAAA
128 ATATTTCGGGTCGGGTATTTTTCACCCTAAACCCGAACCCGACCCGA--CAAATATCACTTAAAA
4803 AAACCGACCCGACCCGACCAAAATAAAGTTT
191 AAACCGACCCGACCCGACCAAAATAAAGTTT
4834 ACCCGACCCGACC
1 ACCCGACCCGACC
4847 TGAATATATG
Statistics
Matches: 218, Mismatches: 11, Indels: 21
0.87 0.04 0.08
Matches are distributed among these distances:
220 39 0.18
222 1 0.00
223 27 0.12
224 25 0.11
225 3 0.01
227 3 0.01
228 5 0.02
229 60 0.28
230 55 0.25
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.28
Consensus pattern (221 bp):
ACCCGACCCGACCCGAAATAATAAAAAAACTATTTTTATTCAATAAAAACAGTGACTTAATTGGA
ATAAAAATATATATAGAGGGGTATTATTGTAATTATTCCTAAATATATAGGTAAAATTATATATA
TTTCGGGTCGGGTATTTTTCACCCTAAACCCGAACCCGACCCGACAAATATCACTTAAAAAAACC
GACCCGACCCGACCAAAATAAAGTTT
Found at i:10710 original size:56 final size:58
Alignment explanation
Indices: 10643--10785 Score: 173
Period size: 56 Copynumber: 2.5 Consensus size: 58
10633 TTTAGGAACC
** *
10643 AAGCCTGATTTTCAAGGGTTTCTTGATGATTATCTCCAAAGAA-TTTTA-AAGAAACT
1 AAGCCTGATTTTCAAGGGTTTCTTGATGACGATCTCCAAAGAATTTTTATAAGAAAAT
* * * * *
10699 AAGCCTAATTTTCAGGGGTTTCTTGATGACGATTTTCAATGAATTTTTATAAGAAAAT
1 AAGCCTGATTTTCAAGGGTTTCTTGATGACGATCTCCAAAGAATTTTTATAAGAAAAT
* * *
10757 AAGCTTGATTTTCAAGGTTTTATTGATGA
1 AAGCCTGATTTTCAAGGGTTTCTTGATGA
10786 GTAATTTCTT
Statistics
Matches: 72, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
56 36 0.50
57 5 0.07
58 31 0.43
ACGTcount: A:0.32, C:0.11, G:0.17, T:0.39
Consensus pattern (58 bp):
AAGCCTGATTTTCAAGGGTTTCTTGATGACGATCTCCAAAGAATTTTTATAAGAAAAT
Found at i:11146 original size:85 final size:85
Alignment explanation
Indices: 10971--11147 Score: 200
Period size: 85 Copynumber: 2.1 Consensus size: 85
10961 TGACGCGCAA
* * * * *
10971 TTGTGTGTCATAAATCTATGACGCGCATTTATGACACGCATTGAGCGTCATTGAAGCCCCCGTCA
1 TTGTGTGTCATAAATCTATGACACGCATGTATGACACACATTGAGCGTCATTGAAGCACACGTCA
*
11036 TAAATGAAGATGGCACACAT
66 TAAATAAAGATGGCACACAT
* * * *
11056 TTGTGTGTCATAAATTTATGACACGCATGTATGACTCACATT-ATGTGTCATTGAAGCACATGTC
1 TTGTGTGTCATAAATCTATGACACGCATGTATGACACACATTGA-GCGTCATTGAAGCACACGTC
*
11120 ATTAAA-AAAGGT-G-ACACAT
65 A-TAAATAAAGATGGCACACAT
*
11139 TCGTGTGTC
1 TTGTGTGTC
11148 GTGATTGTAT
Statistics
Matches: 78, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
83 14 0.18
84 2 0.03
85 58 0.74
86 4 0.05
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (85 bp):
TTGTGTGTCATAAATCTATGACACGCATGTATGACACACATTGAGCGTCATTGAAGCACACGTCA
TAAATAAAGATGGCACACAT
Found at i:15746 original size:42 final size:41
Alignment explanation
Indices: 15673--15778 Score: 126
Period size: 41 Copynumber: 2.5 Consensus size: 41
15663 AACGGTTTCT
15673 TGATGAGTAAGTCCTTGGGCCA-TCAGTAAGTCTTTCGAGCA
1 TGATG-GTAAGTCCTTGGGCCATTCAGTAAGTCTTTCGAGCA
* *
15714 TGATGTGTAAGTCCTATGGGCCATTTA-TAAGTCTTTCGAGTA
1 TGATG-GTAAGTCCT-TGGGCCATTCAGTAAGTCTTTCGAGCA
* *
15756 AGATGATAAGTCCTTCGGGCCAT
1 TGATGGTAAGTCCTT-GGGCCAT
15779 CCATAAGACC
Statistics
Matches: 57, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
40 1 0.02
41 29 0.51
42 25 0.44
43 2 0.04
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (41 bp):
TGATGGTAAGTCCTTGGGCCATTCAGTAAGTCTTTCGAGCA
Found at i:17649 original size:23 final size:23
Alignment explanation
Indices: 17606--17649 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
17596 TTGAGCTCCT
*
17606 GTTATTTTAATTTTTGCATTTTG
1 GTTATTTTAATTTCTGCATTTTG
*
17629 GTTATTGTTTATTTCTG-ATTT
1 GTTATT-TTAATTTCTGCATTT
17650 AGTTGCTAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 10 0.56
24 8 0.44
ACGTcount: A:0.16, C:0.05, G:0.14, T:0.66
Consensus pattern (23 bp):
GTTATTTTAATTTCTGCATTTTG
Found at i:17921 original size:5 final size:5
Alignment explanation
Indices: 17902--17966 Score: 60
Period size: 5 Copynumber: 12.6 Consensus size: 5
17892 ATATTTTAAG
* * * *
17902 TTTAT TTTAA TTTAT TTTAT GTTGT CTTTAT TTTACT TTT-T TTATTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT -TTTAT TTTA-T TTTAT TT-TAT
17949 TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTT
17967 TAAATTGTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
4 3 0.06
5 36 0.73
6 10 0.20
ACGTcount: A:0.17, C:0.03, G:0.03, T:0.77
Consensus pattern (5 bp):
TTTAT
Found at i:17931 original size:26 final size:22
Alignment explanation
Indices: 17902--17966 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 22
17892 ATATTTTAAG
17902 TTTATTTTAATTTATTTTATGTTGT
1 TTTATTTTAATTTATTTTA--TT-T
*
17927 CTTTATTTTACTTT-TTTTATTT
1 -TTTATTTTAATTTATTTTATTT
*
17949 TTTATTTTATTTTATTTT
1 TTTATTTTAATTTATTTT
17967 TAAATTGTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
21 12 0.33
22 5 0.14
23 2 0.06
25 5 0.14
26 12 0.33
ACGTcount: A:0.17, C:0.03, G:0.03, T:0.77
Consensus pattern (22 bp):
TTTATTTTAATTTATTTTATTT
Found at i:17951 original size:16 final size:17
Alignment explanation
Indices: 17932--17967 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
17922 GTTGTCTTTA
17932 TTTTACTTT-TTTTATT
1 TTTTACTTTATTTTATT
*
17948 TTTTATTTTATTTTATT
1 TTTTACTTTATTTTATT
17965 TTT
1 TTT
17968 AAATTGTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.14, C:0.03, G:0.00, T:0.83
Consensus pattern (17 bp):
TTTTACTTTATTTTATT
Found at i:19256 original size:42 final size:40
Alignment explanation
Indices: 19192--19312 Score: 125
Period size: 42 Copynumber: 2.9 Consensus size: 40
19182 ATCGGTTTCT
* *
19192 TGATGAGTAAGTTCTTCAAGCCATCAGTAAGTCTTTCGAGCA
1 TGATG-GTAAGTCCTTCGAGCCATCA-TAAGTCTTTCGAGCA
* * *
19234 TGATGCGTAAGTCCTTTGAGCCATTTATAAGTCTTTCGAGTA
1 TGATG-GTAAGTCCTTCGAGCCA-TCATAAGTCTTTCGAGCA
* * *
19276 TGATGATAAGTCCTTCGGGCCATCCATAAGACTTTCG
1 TGATGGTAAGTCCTTCGAGCCAT-CATAAGTCTTTCG
19313 GGTAGGATTT
Statistics
Matches: 66, Mismatches: 11, Indels: 5
0.80 0.13 0.06
Matches are distributed among these distances:
40 1 0.02
41 25 0.38
42 38 0.58
43 2 0.03
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33
Consensus pattern (40 bp):
TGATGGTAAGTCCTTCGAGCCATCATAAGTCTTTCGAGCA
Found at i:21397 original size:5 final size:5
Alignment explanation
Indices: 21378--21442 Score: 62
Period size: 5 Copynumber: 12.6 Consensus size: 5
21368 GGTTCTCATA
* *
21378 TTTAT GTTTAT TTTAA TTTAT TTTAT GTTGTAT ATTTAT TTTAC TTTAT
1 TTTAT -TTTAT TTTAT TTTAT TTTAT -TT-TAT -TTTAT TTTAT TTTAT
21427 TTTA- -TTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTT
21443 TTTAAATTGT
Statistics
Matches: 50, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
3 3 0.06
5 32 0.64
6 10 0.20
7 5 0.10
ACGTcount: A:0.22, C:0.02, G:0.05, T:0.72
Consensus pattern (5 bp):
TTTAT
Found at i:21420 original size:23 final size:22
Alignment explanation
Indices: 21378--21442 Score: 71
Period size: 23 Copynumber: 2.9 Consensus size: 22
21368 GGTTCTCATA
* *
21378 TTTATGTTTAT-TTTAATTTAT
1 TTTATGTTTATATTTATTTTAC
21399 TTTATGTTGTATATTTATTTTAC
1 TTTATGTT-TATATTTATTTTAC
21422 TTTAT-TTTATTATTTTATTTT
1 TTTATGTTTA-TA-TTTATTTT
21443 TTTAAATTGT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
21 10 0.26
22 7 0.18
23 21 0.55
ACGTcount: A:0.22, C:0.02, G:0.05, T:0.72
Consensus pattern (22 bp):
TTTATGTTTATATTTATTTTAC
Found at i:24010 original size:21 final size:21
Alignment explanation
Indices: 23960--24016 Score: 66
Period size: 19 Copynumber: 2.8 Consensus size: 21
23950 AGAAAATAAT
*
23960 GTAAAAAAA-AAGGAAAAGAAA
1 GTAAAAAAATAA-CAAAAGAAA
*
23981 --AAGAAAATAACAAAAGAAA
1 GTAAAAAAATAACAAAAGAAA
24000 GTAAAAAAATAACAAAA
1 GTAAAAAAATAACAAAA
24017 ATCAAAAATC
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
19 14 0.47
20 2 0.07
21 14 0.47
ACGTcount: A:0.77, C:0.04, G:0.12, T:0.07
Consensus pattern (21 bp):
GTAAAAAAATAACAAAAGAAA
Found at i:28942 original size:5 final size:5
Alignment explanation
Indices: 28923--28982 Score: 66
Period size: 5 Copynumber: 11.2 Consensus size: 5
28913 TAGGTCCTTA
* *
28923 TATTT TATGTT TATTT TATTT TATTT TATGT TATCTT TATTAT TTTTAT
1 TATTT TAT-TT TATTT TATTT TATTT TATTT TAT-TT TATT-T TATT-T
28972 TATTT TATTT T
1 TATTT TATTT T
28983 TTTAATTGTT
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
5 30 0.62
6 18 0.38
ACGTcount: A:0.20, C:0.02, G:0.03, T:0.75
Consensus pattern (5 bp):
TATTT
Found at i:28949 original size:21 final size:22
Alignment explanation
Indices: 28923--28982 Score: 72
Period size: 21 Copynumber: 2.8 Consensus size: 22
28913 TAGGTCCTTA
28923 TATTTTATGTTTATTTTATT-T
1 TATTTTATGTTTATTTTATTAT
28944 TATTTTATG-TTATCTTTATTAT
1 TATTTTATGTTTAT-TTTATTAT
*
28966 TTTTATTAT-TTTATTTT
1 TATT-TTATGTTTATTTT
28983 TTTAATTGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
20 4 0.12
21 15 0.44
22 7 0.21
23 8 0.24
ACGTcount: A:0.20, C:0.02, G:0.03, T:0.75
Consensus pattern (22 bp):
TATTTTATGTTTATTTTATTAT
Found at i:28986 original size:16 final size:16
Alignment explanation
Indices: 28923--28986 Score: 60
Period size: 16 Copynumber: 3.9 Consensus size: 16
28913 TAGGTCCTTA
*
28923 TATTTTATGTTTATT-T
1 TATTTTAT-TTTTTTAT
* *
28939 TATTTTA-TTTTATGT
1 TATTTTATTTTTTTAT
28954 TATCTTTATTATTTTTAT
1 TAT-TTTATT-TTTTTAT
28972 TATTTTATTTTTTTA
1 TATTTTATTTTTTTA
28987 ATTGTTTAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
14 4 0.10
15 4 0.10
16 17 0.43
17 7 0.17
18 8 0.20
ACGTcount: A:0.20, C:0.02, G:0.03, T:0.75
Consensus pattern (16 bp):
TATTTTATTTTTTTAT
Found at i:32977 original size:13 final size:13
Alignment explanation
Indices: 32959--32984 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
32949 CCATTTTTTA
32959 TGACAGTGACGGG
1 TGACAGTGACGGG
32972 TGACAGTGACGGG
1 TGACAGTGACGGG
32985 ATACACATGT
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:0.15, G:0.46, T:0.15
Consensus pattern (13 bp):
TGACAGTGACGGG
Found at i:35210 original size:55 final size:56
Alignment explanation
Indices: 35124--35546 Score: 568
Period size: 55 Copynumber: 7.7 Consensus size: 56
35114 AATGGGTTCA
* * *
35124 CTCCCTATTTCTTTCAG-GCAGTAT-AGAACTCGAATAATCTTCAATAATCGTGTTTG
1 CTCCCTATTTCTTTCAGAG-AGTATGAG-ACTCGAACAATCTTCAACAATCGTGTCTG
**
35180 CTCTTTATTTC-TTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTG
1 CTCCCTATTTCTTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTG
35235 CTCCCTATTTC-TTCA-AGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTG
1 CTCCCTATTTCTTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTG
* *
35289 CTCCCTATTTC-TTCAGAGAGTATAAGACTCGAACAATCTTCAACAATTGTGTCTG
1 CTCCCTATTTCTTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTG
* * *
35344 CTCCCTA-TTCTTTCAGAGAGTATGAGACTTGAACAATCTTCAATAATTGTGTCTG
1 CTCCCTATTTCTTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTG
* *
35399 CTCCCTA-TTCTTTCAGAGAGTATGAGACTCGAACAATCTTCAATAATTGTGTCTG
1 CTCCCTATTTCTTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTG
*
35454 CTCCCTA-TTCTTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGT-TCG
1 CTCCCTATTTCTTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCT-G
* * *
35509 TTCCCTA-TTC-TTCAGGGAGTAT-AGAACTC-AAAAATCTT
1 CTCCCTATTTCTTTCAGAGAGTATGAG-ACTCGAACAATCTT
35547 ATTCTTACGG
Statistics
Matches: 342, Mismatches: 19, Indels: 15
0.91 0.05 0.04
Matches are distributed among these distances:
53 10 0.03
54 73 0.21
55 247 0.72
56 12 0.04
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (56 bp):
CTCCCTATTTCTTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTG
Found at i:35522 original size:219 final size:220
Alignment explanation
Indices: 35124--35531 Score: 614
Period size: 219 Copynumber: 1.9 Consensus size: 220
35114 AATGGGTTCA
* * **
35124 CTCCCTATTTCTTTCAGGCAGTATAGAACTCGAATAATCTTCAATAATCGTGTTTGCTCTTTATT
1 CTCCCTATTTCTTTCAGGCAGTATAGAACTCGAACAATCTTCAATAATCGTGTCTGCTCCCTATT
35189 TCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAAGAG
66 TCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAAGAG
*
35254 TATGAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTC
131 TATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTC
35319 GAACAATCTTCAACAATTGTGTCTG
196 GAACAATCTTCAACAATTGTGTCTG
* *
35344 CTCCCTA-TTCTTTCAGAG-AGTAT-GAGACTTGAACAATCTTCAATAATTGTGTCTGCTCCCTA
1 CTCCCTATTTCTTTCAG-GCAGTATAGA-ACTCGAACAATCTTCAATAATCGTGTCTGCTCCCTA
* *
35406 -TTCTTTCAGAGAGTATGAGACTCGAACAATCTTCAATAATTGTGTCTGCTCCCTA-TTCTTTCA
64 TTTC-TTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTTC-TTCA
* *
35469 GAGAGTATAAGACTCGAACAATCTTCAACAATCGTGT-TCGTTCCCTA-TTCTTCAGGGAGTATA
127 -AGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCT-GCTCCCTATTTCTTCAGAGAGTATA
35532 GAACTCAAAA
Statistics
Matches: 171, Mismatches: 11, Indels: 13
0.88 0.06 0.07
Matches are distributed among these distances:
218 8 0.05
219 113 0.66
220 50 0.29
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.34
Consensus pattern (220 bp):
CTCCCTATTTCTTTCAGGCAGTATAGAACTCGAACAATCTTCAATAATCGTGTCTGCTCCCTATT
TCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAAGAG
TATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTC
GAACAATCTTCAACAATTGTGTCTG
Found at i:35574 original size:54 final size:54
Alignment explanation
Indices: 35516--36300 Score: 1111
Period size: 54 Copynumber: 14.6 Consensus size: 54
35506 TCGTTCCCTA
* * * *
35516 TTCTTCAGGGAGTATAGAACTCAAAAATCTTATTCTTACGGGTTCGTTCCCTCT
1 TTCTTCAGGAAGTATAGAACTCGAAAATCTTCTTCTTACGGGTTCGCTCCCTCT
* * *
35570 TTCTTCAGGAAGTATAGAACTCAAAAAATCTTCTTCTTACGGGTTCCCTCCCCCT
1 TTCTTCAGGAAGTATAGAACTC-GAAAATCTTCTTCTTACGGGTTCGCTCCCTCT
*
35625 TTCTTCAGGAAGTATAGAACTCGAGAATCTTCTTCTTACGGGTTCGCTCCCTCT
1 TTCTTCAGGAAGTATAGAACTCGAAAATCTTCTTCTTACGGGTTCGCTCCCTCT
* *
35679 TTCTTCAGGGAGTATAGAACTCGAATATCTTCTTCTTACGGGTTCGCTCCCTCT
1 TTCTTCAGGAAGTATAGAACTCGAAAATCTTCTTCTTACGGGTTCGCTCCCTCT
*
35733 TTCTTCAGGAAGTATAGAACTCAAAAAATCTTCTTCTTACGGGTTCGCTCCCTCT
1 TTCTTCAGGAAGTATAGAACTC-GAAAATCTTCTTCTTACGGGTTCGCTCCCTCT
* **
35788 TTCTTCAGGAAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCT
1 TTCTTCAGGAAGTATAGAACTCGAAAATCTTCTTCTTACGGGTTCGCTCCCTCT
*
35842 TTCTTCA-GAAGTATAGAACTCAAAAATCTTCTTCTTACGGGTTCGCTCCCTCT
1 TTCTTCAGGAAGTATAGAACTCGAAAATCTTCTTCTTACGGGTTCGCTCCCTCT
* *
35895 TTCTTCAGGAAGTATAGAACTCGAGAATCTTCTTCTTACGGGTTCGCTACCTCT
1 TTCTTCAGGAAGTATAGAACTCGAAAATCTTCTTCTTACGGGTTCGCTCCCTCT
*
35949 TTCTTCAGAAAGTATAGAACTCGAAAATCTTCTTCTTACGGGTTCGCTCCCTCT
1 TTCTTCAGGAAGTATAGAACTCGAAAATCTTCTTCTTACGGGTTCGCTCCCTCT
* * *
36003 TTCTTTAGGAAGTATAGACCTCGAAAATCTTCTTCTTACAGGTTCGCTCCCTCT
1 TTCTTCAGGAAGTATAGAACTCGAAAATCTTCTTCTTACGGGTTCGCTCCCTCT
* * * **
36057 TTTTTCAGGGAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCT
1 TTCTTCAGGAAGTATAGAACTCGAAAATCTTCTTCTTACGGGTTCGCTCCCTCT
* ** *
36111 TTCTTCAGGGAGTATAGAACTCGAAAA---TCTTCAAACGGGTTTGCT-CCTCT
1 TTCTTCAGGAAGTATAGAACTCGAAAATCTTCTTCTTACGGGTTCGCTCCCTCT
**** * *
36161 TTCTTCA-GAGAGTATAGAACTCGAACAATCTTCTGAAAATGGGTTCGCTCGCTCT
1 TTCTTCAGGA-AGTATAGAACTCGAA-AATCTTCTTCTTACGGGTTCGCTCCCTCT
* **
36216 TTCTTCAGGGAGTATAGAACTCGAAAA---TCTTCAAACGGGTTCGCTCCCTCT
1 TTCTTCAGGAAGTATAGAACTCGAAAATCTTCTTCTTACGGGTTCGCTCCCTCT
*
36267 TTCTTCAGGGAGTATAGAACTCGAAAATCTTCTT
1 TTCTTCAGGAAGTATAGAACTCGAAAATCTTCTT
36301 TTGTTCATTT
Statistics
Matches: 663, Mismatches: 55, Indels: 26
0.89 0.07 0.03
Matches are distributed among these distances:
49 1 0.00
50 27 0.04
51 66 0.10
53 49 0.07
54 391 0.59
55 128 0.19
56 1 0.00
ACGTcount: A:0.24, C:0.25, G:0.17, T:0.34
Consensus pattern (54 bp):
TTCTTCAGGAAGTATAGAACTCGAAAATCTTCTTCTTACGGGTTCGCTCCCTCT
Found at i:38283 original size:124 final size:125
Alignment explanation
Indices: 38057--38289 Score: 317
Period size: 124 Copynumber: 1.9 Consensus size: 125
38047 CGCAACATCA
* * *
38057 TCTTATACTGGTACAGGCCTTCAAAATGCCCCAACATATCAGATTGTAAGGCTTACTCTTAATGC
1 TCTTATACTGGTACAGGCCTTCAAAATGCCCCAACACATCAAATTGTAAGGCTCACTCTTAATGC
* *
38122 CTTATTGGTCTAAATCTTGTCCTCTCAATATGATGTGGGTTCAGCTATTCCCCATCAGTG
66 CTCATTGGTCTAAATCTTGTCCTCTCAACATGATGTGGGTTCAGCTATTCCCCATCAGTG
* * ** * * *
38182 TCTTA-ACTGGTACGGGCCTTCAAAATGCCTCGTCACCTCAAATTGTAAGGCTCATTCTTCATGC
1 TCTTATACTGGTACAGGCCTTCAAAATGCCCCAACACATCAAATTGTAAGGCTCACTCTTAATGC
* *
38246 CTCCTTGGTCTGAATCTTG-CCATCTCAACATGATGTGGGTTCAG
66 CTCATTGGTCTAAATCTTGTCC-TCTCAACATGATGTGGGTTCAG
38290 TCGTGCCCCA
Statistics
Matches: 93, Mismatches: 14, Indels: 3
0.85 0.13 0.03
Matches are distributed among these distances:
123 2 0.02
124 86 0.92
125 5 0.05
ACGTcount: A:0.23, C:0.25, G:0.18, T:0.33
Consensus pattern (125 bp):
TCTTATACTGGTACAGGCCTTCAAAATGCCCCAACACATCAAATTGTAAGGCTCACTCTTAATGC
CTCATTGGTCTAAATCTTGTCCTCTCAACATGATGTGGGTTCAGCTATTCCCCATCAGTG
Found at i:39600 original size:17 final size:16
Alignment explanation
Indices: 39580--39619 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 16
39570 CTTCCAATTT
39580 TTTTCTTTTCTTTATTC
1 TTTTCTTTTCTTT-TTC
39597 TTTTCTTTTCTTTTTC
1 TTTTCTTTTCTTTTTC
39613 TCTTTCT
1 T-TTTCT
39620 ACATTTCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 4 0.18
17 18 0.82
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTTCTTTTCTTTTTC
Found at i:42181 original size:21 final size:21
Alignment explanation
Indices: 42157--42211 Score: 85
Period size: 21 Copynumber: 2.6 Consensus size: 21
42147 CAATGAGAAG
42157 TGGTCTTCAT-GTCTTTATGAA
1 TGGTCTTC-TCGTCTTTATGAA
42178 TGGTCTTCTCGTCTTTATGAA
1 TGGTCTTCTCGTCTTTATGAA
*
42199 TGATCTTCTCGTC
1 TGGTCTTCTCGTC
42212 CTTGGTATGA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 1 0.03
21 31 0.97
ACGTcount: A:0.15, C:0.20, G:0.18, T:0.47
Consensus pattern (21 bp):
TGGTCTTCTCGTCTTTATGAA
Found at i:47590 original size:24 final size:25
Alignment explanation
Indices: 47549--47595 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
47539 ACTCAAAAAA
47549 AAAATTAGAAGCTCGATTGAAGTCT
1 AAAATTAGAAGCTCGATTGAAGTCT
* *
47574 AAAATTCG-AGCTTGATTGAAGT
1 AAAATTAGAAGCTCGATTGAAGT
47596 GAAAGAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.38, C:0.11, G:0.21, T:0.30
Consensus pattern (25 bp):
AAAATTAGAAGCTCGATTGAAGTCT
Found at i:48264 original size:22 final size:22
Alignment explanation
Indices: 48236--48283 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
48226 ATAAAATACG
48236 TAAAAATA-AAAATAAATAAAAA
1 TAAAAATATAAAATAAAT-AAAA
* *
48258 TAAAAATATATAATTAATAAAA
1 TAAAAATATAAAATAAATAAAA
48280 TAAA
1 TAAA
48284 TAATGAATCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 16 0.70
23 7 0.30
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (22 bp):
TAAAAATATAAAATAAATAAAA
Found at i:48287 original size:16 final size:17
Alignment explanation
Indices: 48239--48298 Score: 70
Period size: 16 Copynumber: 3.6 Consensus size: 17
48229 AAATACGTAA
48239 AAATAAAAATAAATAA-
1 AAATAAAAATAAATAAT
*
48255 AAATAAAAATATATAAT
1 AAATAAAAATAAATAAT
*
48272 TAAT-AAAATAAATAAT
1 AAATAAAAATAAATAAT
*
48288 GAATCAAAAAT
1 AAAT-AAAAAT
48299 TATATTTTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
16 29 0.78
17 3 0.08
18 5 0.14
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.25
Consensus pattern (17 bp):
AAATAAAAATAAATAAT
Found at i:49318 original size:29 final size:29
Alignment explanation
Indices: 49273--49524 Score: 252
Period size: 29 Copynumber: 8.9 Consensus size: 29
49263 TTAATTTTAC
49273 ATCTTAACATTAAAAATATATTTTATTCTT
1 ATCTTAAC-TTAAAAATATATTTTATTCTT
49303 ATCTTAACTTAAAAATAT-TTTTATTCTT
1 ATCTTAACTTAAAAATATATTTTATTCTT
* *
49331 ATTTTAACTT-AAAA-ATATTTTAGTCTT
1 ATCTTAACTTAAAAATATATTTTATTCTT
*
49358 ATCTTAACTTAAAAATATATTTTATTGTT
1 ATCTTAACTTAAAAATATATTTTATTCTT
* * * *
49387 ATCTTAACTTATACATAAATTATATTCTT
1 ATCTTAACTTAAAAATATATTTTATTCTT
* * *
49416 AACTTTAA-TTATTAAATATATTCTATT-TT
1 ATC-TTAACTTA-AAAATATATTTTATTCTT
* * ** * *
49445 A-CCTAAATT-ATTATATAATTAATTCTT
1 ATCTTAACTTAAAAATATATTTTATTCTT
* *
49472 ATTTTAAATTAAAAAT-T-TTTTATTCTT
1 ATCTTAACTTAAAAATATATTTTATTCTT
49499 ATCTTAACTTAAAAATATATTTTATT
1 ATCTTAACTTAAAAATATATTTTATT
49525 TTAACTAAAA
Statistics
Matches: 182, Mismatches: 29, Indels: 23
0.78 0.12 0.10
Matches are distributed among these distances:
26 11 0.06
27 50 0.27
28 34 0.19
29 63 0.35
30 24 0.13
ACGTcount: A:0.38, C:0.09, G:0.01, T:0.52
Consensus pattern (29 bp):
ATCTTAACTTAAAAATATATTTTATTCTT
Found at i:49523 original size:23 final size:24
Alignment explanation
Indices: 49491--49593 Score: 93
Period size: 23 Copynumber: 4.1 Consensus size: 24
49481 TAAAAATTTT
49491 TTATTCTTATCTTAACTTAAAAATA
1 TTATT-TTATCTTAACTTAAAAATA
*
49516 -TATTTTATTTTAAC-TAAAAATA
1 TTATTTTATCTTAACTTAAAAATA
* *
49538 TTTTTTTATCTTAACTACAAAAAATTA
1 TTATTTTATCTTAACT--TAAAAA-TA
* *
49565 TATATTTTTATCTTAAATTTAAAATA
1 T-TA-TTTTATCTTAACTTAAAAATA
49591 TTA
1 TTA
49594 CTAGAATAAA
Statistics
Matches: 63, Mismatches: 8, Indels: 14
0.74 0.09 0.16
Matches are distributed among these distances:
22 8 0.13
23 21 0.33
24 4 0.06
25 2 0.03
26 8 0.13
27 7 0.11
28 1 0.02
29 12 0.19
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (24 bp):
TTATTTTATCTTAACTTAAAAATA
Found at i:49654 original size:28 final size:26
Alignment explanation
Indices: 49619--49686 Score: 66
Period size: 28 Copynumber: 2.5 Consensus size: 26
49609 AATATTTAAG
*
49619 TAAATAAGAATAATTATATATTTT-ATT
1 TAAATAAGAATAA-AATAT-TTTTAATT
*
49646 TAAAGTAAGATTAAAATATTTTTAAATT
1 TAAA-TAAGAATAAAATATTTTT-AATT
49674 TAAAATAAGAATA
1 T-AAATAAGAATA
49687 TATTTTTAGG
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
26 4 0.12
27 8 0.24
28 19 0.56
29 3 0.09
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (26 bp):
TAAATAAGAATAAAATATTTTTAATT
Done.